John Warner National Defense Authorization Act for Fiscal Year 2007 - Division A: Department of Defense Authorizations - Title I: Procurement - Subtitle A: Authorization of Appropriations - (Sec. 101) Authorizes appropriations for FY2007 for the Army, Navy and Marine Corps, and Air Force for aircraft, missiles, weapons and tracked combat vehicles, ammunition, shipbuilding and conversion, and other procurement. (Sec. 104) Authorizes appropriations for FY2007 for defense-wide procurement. Subtitle B: Army Programs - (Sec. 111) Expresses the sense of Congress that the Secretary of the Army should request from Congress authority to enter into a multiyear procurement contract for the Family of Medium Tactical Vehicles (Family) program, and that such Secretary should submit necessary justification materials for such a contract. Requires any proposal by such Secretary to incorporate improvements from: (1) lessons learned from operations involving the Global War on Terrorism; and (2) product improvement programs carried out for the Family program. (Sec. 112) Authorizes the Secretary of the: (1) Army to enter into a multiyear contract for the procurement of MH-60R helicopters; and (2) Navy to enter into such a contract for MH-60R related mission equipment, both beginning with the FY2007 program year. (Sec. 113) Directs the Secretary of the Army to set forth in Army budget materials for any fiscal year after 2007 all amounts for procurement for the M1A2 Abrams tank system enhancement program and for the Bradley A3 fighting vehicle as elements within amounts requested for the Army's Modular Force Initiative, in accordance with a specified Army report. (Sec. 114) Limits the availability for obligation of funds for FY2007 for the Army's Bridge to Future Networks program until the Secretary of the Army reports to the congressional defense and appropriations committees an analysis of such program and related information. (Sec. 115) Requires a report from the Comptroller General (CG) to the congressional defense and appropriations committees on the participation and activities of the lead systems integrator in the Future Combat Systems (FCS) program. (Sec. 116) Directs the Secretary of Defense (Secretary) to ensure that priority for the distribution of new and combat-serviceable replacement equipment acquired using funds authorized under this title is given to operational units based on combat mission deployment schedule. Subtitle C: Navy Programs - (Sec. 121) Authorizes the Secretary of the Navy to incrementally fund procurement of a CVN-21 class aircraft carrier designated as CVN-78, 79, and 80, as applicable, over four-year periods. (Sec. 122) Provides cost limits, out of Navy shipbuilding and conversion funds, for: (1) the Navy aircraft carrier designated as CVN-21; and (2) any ship of that class that is constructed after the CVN-21. Authorizes the Secretary of the Navy to adjust such amounts based upon specified factors, including inflation, changes in federal, state, or local laws, or the insertion of new technology. Allows technology insertion adjustments only if such Secretary makes specified certifications to the defense and appropriations committees with respect to the need for such technology. Requires such Secretary to notify such committees of any ship cost limit adjustments made. (Sec. 123) Amends the National Defense Authorization Act (NDAA) for Fiscal Year 1998 to increase the cost limitation on the procurement of the CVN-77 aircraft carrier. (Sec. 124) Earmarks specified Navy shipbuilding and conversion funds for construction of the first two vessels under the next-generation destroyer program. Provides contract authority. Expresses the sense of Congress supporting a one-time full funding exception with respect to follow-on ships under such program. (Sec. 125) Provides a cost limit, out of Navy shipbuilding and conversion funds, for any ship constructed under the LHA Replacement amphibious assault ship program. Authorizes the Secretary of the Navy to adjust such amounts based upon specified factors, including inflation, changes in federal, state, or local laws, or the insertion of new technology. Allows technology insertion adjustments only if such Secretary makes specified certifications to the defense and appropriations committees with respect to the need for such technology. Requires such Secretary to notify such committees of any ship cost limit adjustments made. (Sec. 126) Provides cost limits, out of Navy shipbuilding and conversion funds, for specified San Antonio-class naval amphibious ships. Authorizes the Secretary of the Navy to adjust such amounts based upon specified factors, including inflation, changes in federal, state, or local laws, or the insertion of new technology. Allows technology insertion adjustments only if such Secretary makes specified certifications to the defense and appropriations committees with respect to the need for such technology. Requires such Secretary to notify such committees of any ship cost limit adjustments made. (Sec. 127) Authorizes the Secretary of the Navy to enter into a multiyear contract for the procurement of V-22 tiltrotor aircraft, beginning with the FY2008 program year. (Sec. 128) Expresses the sense of Congress that the Navy should make greater use of alternative technologies, including nuclear power, as a means of propulsion for its future fleet of surface combatants. Requires the Secretary of the Navy to include integrated power systems, fuel cells, and nuclear power as propulsion alternatives for future major surface combatant ships. (Sec. 129) Expresses the sense of Congress that the Secretary of the Navy should accelerate the construction of Virginia class submarines to maintain the attack force structure at not less than 48 and to minimize any period that such force remains below 48. (Sec. 130) Directs the Secretary to prescribe a quality control policy for the procurement of: (1) ship critical safety items; and (2) modifications, repair, and overhaul of such items. Subtitle D: Air Force Programs - (Sec. 131) Prohibits the Secretary of the Air Force, before a specified conditional date, from retiring more than 18 B-52 aircraft. Requires such Secretary to maintain not less than 44 of such aircraft as combat-coded aircraft. Prohibits the obligation or expenditure of any Department of Defense (DOD) funds for retiring any of the 93 B-52H aircraft currently in service until 45 days after a report from the Secretary of the Air Force to the defense committees on the amount and type of Air Force bomber force structure. (Sec. 132) Directs the Secretary of the Air Force, as of October 1, 2008, to maintain a total strategic airlift aircraft inventory of not less than 299. (Sec. 133) Prohibits the Secretary of the Air Force from retiring any U-2 aircraft in FY2007. Prohibits retiring such an aircraft after such fiscal year until 60 days following certification to Congress by the Secretary of Defense that the capabilities provided by U-2 aircraft no longer contribute to mitigating any gaps in intelligence, surveillance, and reconnaissance capabilities identified in the 2006 Quadrennial Defense Review. (Sec. 134) Prohibits the Secretary of the Air Force from using incremental funding for the procurement of F-22A fighter aircraft. Authorizes such Secretary to enter into a multiyear contract for procurement of up to 60 F-22A Raptor fighter aircraft, beginning with the FY2007 program year. Outlines certification requirements with respect to such procurement. Requires the Secretary of Defense to provide for a federally funded research and development center to report cost estimates for a three-year, 60-aircraft, F-22A multiyear procurement program, beginning in FY2007, compared to a corresponding annual procurement program. (Sec. 135) Prohibits the number of: (1) KC-135E aircraft retired by the Secretary of the Air Force during FY2007 from exceeding 29; and (2) F-117A aircraft retired by the Secretary of the Air Force during FY2007 from exceeding ten. (Sec. 137) Prohibits the number of C-130E tactical airlift aircraft retired by the Air Force during FY2007 from exceeding 51. (Sec. 138) Requires any Joint Primary Aircraft Training System aircraft procured after FY2006 to be procured through a contract under provisions of the Federal Acquisition Regulation (FAR) relating to acquisition by negotiated contract rather than FAR provisions relating to the acquisition of commercial items. (Sec. 139) Directs the Air Force to modernize Minuteman III intercontinental ballistic missiles (ICBMs) in U.S. inventory in order to maintain a sufficient supply of launch test assets and spares to sustain the deployed force of such missiles through 2030. Prohibits the obligation or expenditure of DOD funds for the termination of any Minuteman III ICBM modernization program, or for the withdrawal of any such missile from the active force, until 30 days after the Secretary reports to the defense and appropriations committees certain justifications, analyses, and assessments with respect to the Minuteman III ICBM. Subtitle E: Joint and Multiservice Matters - (Sec. 141) Amends the NDAA for Fiscal Year 2006 to state that a limitation on the use of DOD funds for the procurement of a new unmanned aerial vehicle system applies only to DOD procurement funds. Title II: Research, Development, Test, and Evaluation - Subtitle A: Authorization of Appropriations - (Sec. 201) Authorizes appropriations for FY2007 for the Armed Forces for RDT&E. Earmarks specified amounts for the Defense Science and Technology Program. Subtitle B: Program Requirements, Restrictions, and Limitations - (Sec. 211) Earmarks specified Navy and Air Force funds for continued development of an alternate engine for the Joint Strike Fighter (Fighter). Directs the Secretary to: (1) provide for development and procurement of the Fighter propulsion system through the development and sustainment of two interchangeable propulsion systems; and (2) notify the defense and appropriations committees prior to any modification of the Fighter acquisition program that would result in propulsion system development or procurement in a manner other than the above process. Requires independent cost analyses of the Fighter's engine program by the CG, a federally funded research and development center, and the Secretary (with results reports by each to the defense and appropriations committees). (Sec. 212) Authorizes the Director of Defense Research and Engineering and the service acquisition executives of the military departments (currently, only the Director of the Defense Advanced Research Projects Agency) to award prizes for advanced technology achievements within their respective departments. Extends such program through FY2010. Modifies related reporting requirements. (Sec. 213) Requires the Secretary, in response to a critical cost growth threshold breach in a major defense acquisition program (MDAP) under the Defense Acquisition Challenge Program, to address any design, engineering, manufacturing, or technology integration issues that contributed significantly to the cost growth of the MDAP. Directs the Under Secretary of Defense for Acquisition, Technology, and Logistics (Under Secretary) to: (1) establish procedures for the prompt issuance of a solicitation for challenge proposals addressing such cost growth increases; and (2) establish guidelines for covering the costs of the challenge proposals. Outlines authorized actions upon unfavorable full review and evaluation of challenge proposals. Requires the Under Secretary to: (1) evaluate incentives for encouraging the adoption of challenge proposals receiving favorable full review and evaluations, as well as possible additional incentives; and (2) report evaluation results to the defense committees. Authorizes the Under Secretary to establish procedures to ensure that the Challenge Program establishes appropriate priorities for proposals from businesses that are not major contractors with DOD. Extends the Challenge Program through FY2012. (Sec. 214) Requires the Secretary, 120 days after the preliminary design review of the FCS program, to carry out a Defense Acquisition Board milestone review of such program, including a determination as to whether the program should continue. Requires a report from the Secretary to the defense and appropriations committees on review findings and conclusions. Prohibits the obligation of program funds beginning in FY2009 until such report is received. (Sec. 215) Earmarks specified defense-wide RDT&E funds to implement or evaluate certain Navy shipbuilding technology proposals under the Defense Acquisition Challenge Program. (Sec. 216) Directs the Secretary to: (1) provide for an independent estimate by a federally funded research and development center of anticipated costs of systems development and demonstration with respect to the FCS; and (2) report the estimate to the defense and appropriations committees. (Sec. 217) Amends the NDAA for Fiscal Year 2000 to extend through FY2012 the funding objectives of its defense science and technology programs. Outlines actions, including additional reports to the defense and appropriations committees, required of the Secretary following failure to comply with such objectives. (Sec. 218) Directs the Secretary to establish within DOD a joint technology office on hypersonics in order to carry out a program for the development of hypersonics for defense purposes. Requires: (1) the office to develop a roadmap for DOD hypersonics programs; (2) the Secretary to submit the roadmap to the defense and appropriations committees; and (3) the office to annually review and certify consistent funding for research, development, test, evaluation, and demonstration programs within DOD for hypersonics. (Sec. 219) Requires the Secretary to submit to the defense and appropriations committees a proposal to replace nuclear warheads on 24 Trident D-5 sea-launched ballistic missiles with conventional kinetic warheads. Subtitle C: Missile Defense Programs - (Sec. 221) Allows FY2007 and FY2008 RDT&E funds for the Missile Defense Agency (MDA) to be used for the development and fielding of ballistic missile defense capabilities. (Sec. 222) Prohibits any DOD funds from being obligated or expended for the testing or deployment of a space-based interceptor until 90 days after a report from the MDA Director to the defense and appropriations committees. (Sec. 223) States as the policy of the United States that DOD accord a priority within its missile defense program to the development, testing, fielding, and improvement of specified near-term missile defense capabilities. (Sec. 224) Amends the NDAA for Fiscal Year: (1) 2002 to extend by one year CG assessments of ballistic missile defense (BMD) programs; and (2) 2006 to provide submittal dates of plans for test and evaluation of the operational capability of the BMD system. (Sec. 226) Requires annual reports, from 2007 through 2013, from the Under Secretary to the defense and appropriations committees on DOD plans for the transition of missile defense programs from the MDA to the military departments. Subtitle D: Other Matters - (Sec. 231) Requires that if, before a final decision is made within DOD to proceed with a MDAP beyond low-rate initial production, a decision is made to proceed to operational use of the MDAP or to make procurement funds available for that MDAP, then the Director of Operational Test and Evaluation shall submit to the Secretary and the defense and appropriations committees a report with respect to the MDAP. Directs the Under Secretary and such Director to: (1) review DOD policies and practices on test and evaluation in light of emerging approaches to acquisitions; and (2) if necessary, issue new or revised guidance for DOD on test and evaluation. Requires the Director of the Defense Test Resource Management Center to ensure that the DOD strategic plan for test and evaluation resources reflects any DOD testing needs identified in the review, and includes an assessment of the resources and budgets required to meet such needs. Requires the Under Secretary and the Director of Operational Test and Evaluation to submit a review report to the defense and appropriations committees. (Sec. 232) Extends through the end of FY2011 the Global Research Watch Program carried out by DOD's Director of Defense Research and Engineering. (Sec. 233) Expresses the sense of the Senate that the Secretary should share U.S. joint strike fighter technology with the government of the United Kingdom consistent with national security interests of both nations. (Sec. 234) Directs the Secretary to contract with an appropriate independent entity to assess various foreign and domestic vehicle-based active protection systems for defense against certain battlefield threats. Requires a results report from the entity chosen to the Secretary and the defense and appropriations committees. Title III: Operation and Maintenance - Subtitle A: Authorization of Appropriations - (Sec. 301) Authorizes appropriations for FY2007 for operation and maintenance (O&M) for the Armed Forces and specified activities and agencies of DOD. (Sec. 302) Authorizes appropriations for FY2007 for: (1) working capital funds; (2) the Defense Health Program; (3) chemical agents and munitions destruction; (4) defense drug interdiction and counter-drug activities; and (5) the Defense Inspector General. Subtitle B: Environmental Provisions - (Sec. 311) Establishes required qualifications for the DOD position of unexploded ordnance manager. (Sec. 312) States that the two-year limitation for cooperative agreements entered into for environmental restoration at defense facilities shall not apply when the agreement is funded out of either the Department of Defense Base Closure Account 1990 or the Department of Defense Base Closure Account 2005. (Sec. 313) Directs DOD to set certain performance goals for the remediation unexploded ordnance, discarded military munitions, and munitions constituents (munitions) at all active military installations and formerly used defense sites (other than operational ranges). Requires the Secretary to submit to the defense and appropriations committees: (1) a comprehensive plan for addressing the remediation of such munitions at all such sites; (2) specified updates to such plan; and (3) a report on the status of DOD efforts to achieve agreement with relevant regulatory agencies on appropriate munitions reuse standards or principles. (Sec. 314) Requires the Secretary to: (1) conduct a historical review of the number, size, and probable locations where the Armed Forces disposed of military munitions in coastal waters; (2) periodically release any new information obtained during such review; (3) include such information in the annual report on DOD environmental restoration activities submitted to Congress under current law; (4) complete the historical review and submit a final findings report to Congress; (5) provide information obtained in the review to the Secretary of Commerce to assist the National Oceanic and Atmospheric Administration (NOAA) in preparing nautical charts and other navigational materials that identify known or potential hazards posed by such disposed munitions; (6) continue to inform potentially affected users of the ocean environment of such possible hazards; (7) continue to conduct research on the effects of such disposed munitions on ocean environment and those who use it; and (8) institute monitoring mechanisms if the review or research indicates that contamination is being released into ocean waters from disposed munitions at a particular site or that the site poses a significant public health or safety risk. (Sec. 315) Authorizes the Secretary to transfer specified funds to the Moses Lake Wellfield Superfund Site, Washington, to reimburse the Environmental Protection Agency (EPA) for costs incurred in overseeing a remedial investigation and feasibility study performed by the Army. (Sec. 316) Requires the Secretary of the Army to transport to an authorized disposal facility all of the federal government-furnished uranium in the chemical and physical form in which it is stored at the Sequoyah Fuels Corporation site in Gore, Oklahoma. (Sec. 317) Amends the Toxic Substances Control Act to authorize the EPA Administrator to extend an exemption from certain toxic disposal requirements for up to 60 days to allow the Secretary and the military department Secretaries to transport polychlorinated biphenyls generated by or under control of DOD inside the United States for their disposal, treatment, or storage, as long as the Administrator determines that they would not otherwise arrive within the period of the original exemption. Terminates such authority on September 30, 2012. Requires a report from the Secretary to the defense and environmental affairs committees on the status of foreign-manufactured polychlorinated biphenyls under DOD control outside the United States. (Sec. 318) Requires the Secretary of the Navy to enter into an agreement with the National Academy of Sciences to conduct a review and evaluation of scientific and medical evidence regarding associations between pre-natal, child, and adult exposure to contaminated drinking water at Camp Lejeune, North Carolina, and birth defects or diseases and any other adverse health effects. Directs the: (1) Academy to submit review results to the Secretary and Congress; and (2) Commandant of the Marine Corps, after completion of a related study, to provide study results to former Camp Lejeune residents and employees who may have been exposed to such drinking water. Subtitle C: Program Requirements, Restrictions, and Limitations - (Sec. 321) Prohibits the Secretary from obligating or expending funds for any financial management improvement activity relating to the preparation, processing, or auditing of financial statements until the Secretary makes certain determinations to the defense and appropriations committees with respect to each activity proposed to be funded. (Sec. 322) Earmarks specified Army O&M funds for contracts for the acquisition, installation, and maintenance of exhibits at the National Museums of the United States Army, United States Navy, Marine Corps and Heritage Center, and United States Air Force. Authorizes the Secretary of the military department concerned (Secretary concerned) to accept from nonprofit entities amounts as reimbursement for costs at such Museums. (Sec. 323) Directs the Secretary to ensure that financial resources are provided to enable: (1) the Secretary concerned to meet requirements for the repair, recapitalization, and replacement of equipment used in the global war on terrorism; and (2) the Secretary of the Army to meet Army requirements for transforming to modularity, as well as the reconstitution of equipment and materiel in prepositioned stocks under the Army Prepositioned Stocks Strategy 2012 or any subsequent strategy. Requires the: (1) Secretary to report annually to Congress with respect to budget requirements necessary to meet the above requirements; (2) Secretary of the Army to report to the defense and appropriations committees on progress made in meeting the Army requirements; and (3) CG to report to such committees assessing the Army's progress. (Sec. 324) Prohibits the Secretary of the Navy from deploying the Marine Corps Total Force System to the Navy until the date on which the defense and appropriations committees and the Secretary of the Navy receive the determination of the Chairman of the Defense Business Systems Management Committee that such deployment is in the best interests of DOD. Requires a report from: (1) such Secretary to such committees and the CG analyzing alternatives, costs and benefits, and compatability aspects of such System; and (2) the CG to such committees and such Chairman assessing such Secretary's report. Subtitle D: Workplace and Depot Issues - (Sec. 331) Makes permanent (currently limited to contracts entered into during FY2003-FY2009) the exclusion of certain contract expenditures from percentage limitations on the performance of depot-level maintenance by non-federal contractor personnel at a DOD Center of Industrial and Technical Excellence. (Sec. 332) Requires the Secretary of a military department to invest in the capital budgets of the covered depots in that department at least six percent of the total combined workload funded at all the covered depots of that department for the preceding three fiscal years. Allows a waiver of such minimum investment for national security reasons if the Secretary of Defense notifies the defense and appropriations committees. Requires an annual report from the Secretary to such committees summarizing the level of capital investment for each military department for the preceding fiscal year. Specifies the depots covered. Provides a two year phase-in of the investment requirement with respect to the Army and Navy. (Sec. 333) Amends the Bob Stump NDAA for Fiscal Year 2003 (Stump Act) to extend through FY2009 the temporary authority to contract for increased performance of security guard functions. Provides FY2007-FY2009 limits on the total number of personnel authorized to perform such functions. Requires a report from the Secretary to the defense committees on contractor performance of security guard functions under such Act, and prohibits any such contract from being entered into after September 30, 2007, until the report is submitted. Subtitle E: Reports - (Sec. 341) Directs the Secretary of the Navy to report to the defense committees on the Navy's Fleet Response Plan. Requires a follow-up report from the CG containing a review of the Navy report. Prohibits such Secretary from expanding implementation of the Plan beyond the carrier strike groups until six months after such report is submitted. (Sec. 342) Requires a report from the Secretary of the Navy to the defense committees on Navy surface ship rotational crew programs. Prohibits such Secretary from implementing any new surface ship rotational crew experiment or program during the period beginning on the date of enactment of this Act and ending on October 1, 2009. Provides for the treatment of four existing rotational crew experiments. Requires a follow-up report from the CG on an existing experiment known as the "sea swap." Requires the Director of the Congressional Budget Office (CBO) to report to the defense committees on the long-term implications of the use of crew rotations on Navy ships on the degree of forward presence provided by Navy ships. (Sec. 343) Directs the Secretary of the Army to report to Congress on the adequacy of the live-fire Army ranges in Hawaii with respect to current and future training requirements. (Sec. 344) Requires a report from the CG to the defense committees assessing the joint standards and protocols for access control systems at DOD installations. (Sec. 345) Directs the CG to report to the defense committees on the readiness of the active and reserve ground forces of the Army and Marine Corps. (Sec. 346) Directs the Secretary of the Air Force to report to the defense and appropriations committees on Air Force safety requirements for flight training operations at Pueblo Memorial Airport, Colorado. (Sec. 347) Requires: (1) annual reports from the Secretary to Congress on future DOD requirements with respect to the Personnel Security Investigations for Industry and the National Industrial Security Program of the Defense Security Service; and (2) a follow-up report from the CG after the Secretary's initial report. (Sec. 348) Amends the Stump Act to extend through FY2013 an annual reporting requirement on the DOD training range sustainment plan and inventory. (Sec. 349) Requires: (1) a report from the Secretary concerned to the Secretary within 90 days after withdrawing equipment from a reserve unit to a unit being ordered to active duty or to a unit for the discharge of a mission; and (2) quarterly reports from the Secretary to Congress on all such reports submitted. Subtitle F: Other Matters - (Sec. 351) Directs the Secretary to: (1) maintain a strategic policy on DOD programs for the prepositioning of materiel and equipment; (2) notify the defense and appropriations committees prior to implementing any policy change; and (3) establish the strategic policy within six months after the enactment of this Act. Prohibits the Secretary, from the date of enactment of this Act until the date on which policy change notification is submitted, from diverting materiel or equipment from prepositioned stocks except for directly supporting a contingency operation or providing humanitarian assistance. (Sec. 352) Makes both military dogs (current law) and horses available for adoption at the end of their useful working life. (Sec. 353) Authorizes the Secretary of the Army to carry out a program to sell recyclable munitions materials resulting from the demilitarization of conventional military munitions and to use such proceeds for the reclamation, recycling, and reuse of such munitions. (Sec. 354) Authorizes the Secretary of the Army to recover from any country to which a grant of rifles, ammunition, repair parts, or other related supplies (munitions) is made under provisions of the Foreign Assistance Act of 1961 any such munitions that are excess to the needs of such country. Makes such munitions available for transfer to the Corporation for the Promotion of Rifle Practice and Firearms Safety. (Sec. 355) Amends the NDAA for Fiscal Year 2004 to extend the termination date for the DOD telecommunications benefit under such Act from September 30, 2006, to 60 days after the date on which the Secretary determines that a contingency operation has ended. Extends such benefit to members who remain hospitalized as a result of wounds or injuries incurred while in direct support of a contingency operation, up until the end of such operation. Directs the Secretary to report to the defense committees on the implementation of the modified benefit. (Sec. 356) Amends the NDAA for Fiscal Year 2006 to extend through FY2007 the availability of funds for activities associated with the commemoration of success of the U.S. Armed Forces in Operations Enduring Freedom and Iraqi Freedom. (Sec. 357) Requires the Secretary to: (1) perform an annual accounting of DOD overseas staffing requirements in order to reconcile staffing cost-sharing fees levied by the Secretary of State under the Secure Embassy Construction and Counterterrorism Act of 1999; and (2) submit to the defense and appropriations committees an annual estimate of overseas military presence. (Sec. 358) Directs the Secretary to consider the utilization of fuel cells as replacements for current back-up power systems in a variety of DOD operations and activities. (Sec. 359) Authorizes the Secretary to: (1) consult with the Secretary of Homeland Security and state governments in developing concept plans for providing DOD support to civil authorities; and (2) provide for the prepositioning of pre-packaged or pre-identified basic response assets in order to improve such support. (Sec. 360) Requires a report from the Secretary to the defense and appropriations committees on DOD progress in implementing its policy to improve the fuel efficiency of weapons platforms, consistent with mission requirements. (Sec. 361) Expresses the sense of Congress that: (1) the President's budget for FY2007 failed to fund the required number of ship steaming days per quarter for Navy ship operations as well as deferring projected depot maintenance for Navy ships and aircraft; and (2) the Secretary should ensure sufficient funding to support critical Navy training and depot maintenance accounts for readiness purposes. Directs the: (1) Secretary to certify to the defense and appropriations committees, for each of FY2008-FY2010, that the Navy has funding to fully meet such requirements; (2) Secretary of the Navy, during those same fiscal years, to report to such committees on progress made in achieving such funding; and (3) Secretary of the Navy to report to such committees on the Navy Riverine Squadrons. (Sec. 362) Requires the Secretary concerned to provide, under certain conditions, adequate storage of personal possessions belonging to military personnel residing in military family housing who are assigned to a family-restricted area for a period of 180 days or more. (Sec. 363) Requires (current law authorizes) the Secretary to include in contracts for the transportation of baggage and household effects for members of the Armed Forces (current law) and civilian DOD employees a clause requiring the carrier to pay the full replacement value of lost or damaged goods. Directs the: (1) Secretary to report to the defense and appropriations committees on the capabilities and costs of the DOD program known as the "Families First" program; and (2) CG to conduct a review and assessment, and submit an interim and final report to the defense committees, with respect to DOD progress in achieving the goals of the Families First program, as well as related matters. Title IV: Military Personnel Authorizations - Subtitle A: Active Forces - (Sec. 401) Sets forth authorized end strengths for active-duty forces as of the end of FY2007. (Sec. 402) Revises the permanent active-duty end strength minimum levels for the Army, Navy, Marine Corps, and Air Force. (Sec. 403) Amends the Ronald W. Reagan NDAA for Fiscal Year 2005 (Reagan Act) to authorize additional increases of active-duty end strengths for the Army and Marine Corps in FY2008 and FY2009 in order to support operational missions and achieve transformational reorganization objectives. Subtitle B: Reserve Forces - (Sec. 411) Sets forth authorized end strengths as of the end of FY2007 for members of the Selected Reserve and reserve personnel on active duty in support of the reserves. (Sec. 413) Sets forth minimum end strengths for FY2007 for Army and Air Force dual status military technicians. (Sec. 414) Provides a FY2007 limitation on the number of non-dual status Army and Air Force military technicians. (Sec. 415) Provides, during FY2007, the maximum number of reserve personnel authorized to be on active duty for operational support. Subtitle C: Authorization of Appropriations - (Sec. 421) Authorizes appropriations for FY2007 for: (1) military personnel; and (2) the Armed Forces Retirement Home. Title V: Military Personnel Policy - Subtitle A: Officer Personnel Policy - Part I: Officer Personnel Policy Generally - (Sec. 501) States that general and flag officers assigned to senior level intelligence positions within the Central Intelligence Agency (CIA) and the Office of the Director of National Intelligence shall not be subject to the supervision or control of the Secretary of Defense and shall not exercise supervision or control over DOD military or civilian personnel. Provides that an officer's appointment to such a position shall not affect the officer's status, grade, rank, compensation, rights, or benefits, and that such officer's pay and allowances shall be reimbursed to DOD from funds available to the CIA or the Office of the Director of National Intelligence. (Sec. 502) Increases from 62 to 64 the mandatory retirement age for general and flag officers. Authorizes the: (1) Secretary to defer the retirement of officers serving in grades above major general and rear admiral until age 66; and (2) President to defer the retirement for such officers until age 68. Eliminates the numerical limit on the number of deferments that may be in effect at any one time. (Sec. 503) Increases the mandatory retirement age for: (1) major generals and rear admirals from 62 to 64; (2) brigadier generals and rear admirals (lower half) and all officers below such grades from 60 to 62; and (3) officers holding certain positions (chiefs of the reserves and National Guard, and state adjutant generals) from 64 to 66. (Sec. 504) Requires the officer serving as the senior Air Force dental officer to be appointed in the grade of major general (currently, brigadier general). (Sec. 505) Authorizes the Secretary concerned to retain chief warrant officers (W-4) who have twice failed for promotion without a mandatory selective continuation board (as required under current law). Allows such warrant officers retained on active duty to be further considered for promotion. (Sec. 506) Extends through October 1, 2008, the temporary reduction of the time-in-grade requirement before eligibility for promotion for certain active-duty officers in the grades of first lieutenant and lieutenant (junior grade). (Sec. 507) States that an active-duty or reserve officer serving as Attending Physician to the Congress shall: (1) hold the grade of major general or rear admiral during such service; and (2) be exempt from end strength and distribution limits for officers serving in grades above brigadier general or rear admiral (lower half). (Sec. 508) Revises the qualifications for leadership of the Naval Postgraduate School to allow in such position: (1) an officer in the Marine Corps (currently, only the Navy); or (2) a civilian, including an individual retired from the Navy or Marine Corps in a grade not below captain or colonel, respectively. Part II: Officer Promotion Policy - (Sec. 511) Revises military promotion procedures to treat a promotion that requires Senate confirmation as being established upon approval by the President of a report of a selection board. Directs the Secretary (currently, the Secretary concerned), by March 1, 2008, to prescribe regulations controlling delays in appointment following Senate confirmation. Provides additional bases for delays in such appointments due to lack of qualifications. (Sec. 512) Prohibits a promotion selection board from recommending an officer for promotion unless a majority of board members, after consideration of any adverse information, finds that the officer is among those best qualified for promotion to meet the needs of the department concerned. (Sec. 513) Authorizes the Secretary and the Deputy Secretary of Defense (currently, only the President) to remove the name of an officer from the report of a selection board with respect to officers being recommended for promotion to grades below brigadier general and rear admiral (lower half). (Sec. 514) Limits the availability of specialty selection boards to officers who are in or above the promotion zone. (Sec. 515) Provides that, if an officer whose name is on a list of officers approved for promotion which requires the advice and consent of the Senate is not appointed during that officer's promotion eligibility period (generally 18 months after being put on the promotion list), then the officer's name shall be removed from the list. Allows the President to extend the promotion eligibility period by an additional 12 months. Provides the same requirements with respect to officers on the reserve active status list. Part III: Joint Officer Management Requirements - (Sec. 516) Revises the system for the designation and management of joint qualified officers (JQOs) to replace the term "joint specialty officer" with "joint qualified officer." Requires the Secretary to establish different levels of joint qualification, as well as the criteria for qualification at each level, and requires each level to have joint education and joint experience criteria. Allows an officer to be designated as a JQO only if the officer successfully completes an appropriate program of joint professional military education and also successfully completes: (1) a full tour of duty in a joint assignment; or (2) such other assignments and experiences that demonstrates the officer's mastery of knowledge, skills, and abilities in joint matters (as prescribed by the Secretary). (Currently, an officer can only qualify if he or she completes such education and a full tour of duty in a joint assignment.) Authorizes the Secretary to waive the educational requirement in certain instances upon a determination that the officer has demonstrated joint knowledge, skills, and abilities, or when determined necessary to meet a critical need. Provides JQO numerical limits. Makes this section effective as of October 1, 2007. Requires the Secretary to submit to the defense committees a plan for implementation of the joint officer management system. (Sec. 517) Repeals the requirement for a separate promotion policy objective for joint officers. States as the policy objective that officers who are serving or have served in joint duty assignments are expected, as a group, to be promoted to the next higher grade at a rate not less than that for all officers of that armed force in that grade and competitive category. (Sec. 518) Limits joint professional military education schools to schools under the National Defense University. Includes within such schools the National War College, the Industrial College of the Armed Forces, and the Joint Forces Staff College. (Sec. 519) Revises the definition of the term "joint matters" to mean matters related to the achievement of unified action by multiple military forces in operations conducted across land, sea, air, space, or the information environment. Includes under the definition of "critical occupational specialty" any occupational specialties within combat arms or its equivalent that the Secretary determines are experiencing severe shortages of trained officers. Subtitle B: Reserve Component Matters - Part I: Reserve Component Management - (Sec. 521) Recognizes and commends former Representative G. V. "Sonny" Montgomery for his 30 years of service to benefit the people of Mississippi, members of the Armed Forces and their families, veterans, and the United States. (Sec. 522) Extends from 270 to 365 days the maximum duration of service for members of the Selected Reserve and Individual Ready Reserve called involuntarily to active duty to support operational missions. Requires, in determining which members will be ordered to active duty without their consent, appropriate consideration to be given to: (1) the length and nature of previous service; (2) the frequency of assignments; (3) family responsibilities; and (4) employment necessary to maintain the national health, safety, or interest. (Sec. 523) Amends the NDAA for Fiscal Year 2006 to authorize military retirement credit for emergency response service performed in specified New Jersey counties immediately after the terrorist attacks of September 11, 2001, by members of the Army or Air National Guard. Part II: Authorities Relating to Guard and Reserve Duty - (Sec. 525) Authorizes reserve personnel performing active Guard and reserve duty and military technicians (dual status) to also instruct or train active-duty personnel, members of foreign military forces, and DOD contractor personnel and civilian employees, as long as such instruction or training is performed in the United States, its possessions, or Puerto Rico. (Sec. 526) Authorizes the governor of a state, Puerto Rico, or the Virgin Islands, or the commanding general of the District of Columbia National Guard, to order a member of their National Guard to perform active Guard and reserve duty, including support of operations or missions and support of training operations and missions. (Sec. 527) Includes under the types of emergencies to which reserve personnel assigned to weapons of mass destruction civil support teams may respond to: (1) a natural or manmade disaster in the United States; or (2) the intentional or unintentional release of nuclear, biological, radiological, or toxic or poisonous chemicals in the United States that results or could result in the catastrophic loss of life or property. (Sec. 528) Amends the NDAA for Fiscal Year 2005 to authorize the Chairman of the Commission on the National Guard and Reserves to exercise with Commission members the same waiver regarding annuity eligibility upon reemployment as that available for the Director of the Office of Personnel Management (OPM) with respect to former federal employees. Extends a Commission final report submission date. (Sec. 529) Requires, as additional matters to be reviewed by the above Commission: (1) National Guard enhancement proposals; (2) a higher rank for the Chief of the National Guard Bureau; (3) National Guard officers authority to command; and (4) National Guard equipment and funding requirements. Requires Commission priority review with respect to the grade and functions of the Chief, and requires a report from the Commission to the defense committees on the results of the priority review. Subtitle C: Education and Training - Part I: Service Academies - (Sec. 531) Increases from 24 to 100 the number of: (1) cadets and midshipmen at the military academies who may participate in exchange programs with foreign military academies; and (2) students from foreign military academies who may receive instruction at a U.S. military academy. Increases the annual funding for each of the military departments for such programs. Authorizes academies to use funds other than appropriated funds in support of such programs. (Sec. 532) Codifies under federal armed forces provisions a section of the NDAA for Fiscal Year 2004 concerning DOD actions to address sexual harassment and violence at the service academies. (Sec. 533) Directs the Secretary to prescribe DOD policy on service academy and ROTC graduates seeking to participate in professional sports before the completion of their active-duty service obligation. Requires military department Secretaries, by December 1, 2007, to amend current or prescribe new regulations to implement the policy prescribed by the Secretary. Part II: Scholarship and Financial Assistance Programs - (Sec. 535) Authorizes members of the Reserve Officers' Training Corps (ROTC) who participate in the Guaranteed Reserve Forces Duty scholarship program to participate in the Health Professions scholarship program and serve on active duty as required by the latter program. (Sec. 536) Authorizes each department Secretary to detail commissioned officers as students at accredited medical schools or schools of osteopathy in the United States for a period of training leading to the degree of doctor of medicine. Prohibits more than 25 officers from each military department from commencing such training in a fiscal year. Outlines eligibility requirements, including having served on active duty for a period of not less than two years nor more than six years, and agreeing to serve as a medical officer in that military department when such training is completed. Allows a portion of the service requirement to be performed in the Selected Reserve. (Sec. 537) Increases from $22,000 to $60,000 the maximum amount of repayment by the Secretary under the education loan repayment program for officers in specified military health care professions. (Sec. 538) Increases the monthly stipend and annual grant amounts under the Health Professions Scholarship and Financial Assistance Program. Requires a Program report from the Secretary to Congress. Prohibits any additional adjustments during FY2007. Part III: Junior ROTC Program - (Sec. 539) Requires that, in order for a retired or noncommissioned officer to be employed as a Junior ROTC (JROTC) instructor, the officer must be certified by the Secretary concerned as a qualified instructor in leadership, wellness and fitness, civics, and other courses related to JROTC program content. Requires senior military instructors to be retired officers and to serve as instructional leaders who oversee the program. Outlines senior military instructor qualifications. Requires non-senior military instructors to be retired noncommissioned officers and to serve as instructional leaders who teach independently of, but share program responsibilities with, senior military instructors. Outlines non-senior military instructor qualifications. (Sec. 540) Authorizes the Secretary concerned to allow retired National Guard and reserve officers to provide JROTC instruction. Directs the Secretary concerned to pay to the educational institution at which the instruction is provided one-half of the amount paid by the institution to the officer for any period up to a maximum of one-half of the difference between the retired pay for an active duty officer of the same grade and years of service for such period and the active duty pay and allowances which the former officer would have received for such period if on active duty. (Sec. 541) Requires the military department Secretaries to increase the number of secondary educational institutions at which a unit of the JROTC is organized. Outlines expansion within the various military departments. (Sec. 542) Directs the Secretary to: (1) conduct a review of a specified legal opinion issued by the DOD General Counsel regarding instruction of non-host unit students participating in JROTC programs; and (2) report review results to the defense committees. Allows a host school that is currently providing for the assignment of JROTC instructors to another school with 70 or more students to continue such support until 180 days following the committees' receipt of such report. Part IV: Other Education and Training Programs - (Sec. 543) Allows all enlisted members (currently, only enlisted members of the Navy and Marine Corps) to participate in certain programs and courses offered by the Naval Postgraduate School in furtherance of the performance of required duties. Authorizes the Secretary to allow an enlisted member to receive graduate-level instruction at such School in a program leading to a master's degree in a technical, analytical, or engineering curriculum. Revises or repeals certain related report requirements under the NDAA for Fiscal Year 2006. Requires a new report from the Secretaries of the Navy and Air Force on the manner in which each Secretary intends to use such School during fiscal years 2008 through 2013 to meet the requirements of enlisted members with graduate degrees. Subtitle D: General Service Authorities - (Sec. 546) Requires the Secretary to: (1) conduct a test of the utility of commercially available test preparation guides and education programs designed to assist recruit candidates to achieve scores on military recruit qualification testing that better reflect their full potential; and (2) report to the defense committees on test findings. (Sec. 547) Prohibits the proceedings of selection boards convened for active-duty and reserve personnel actions (promotion, retention, retirement, etc.) from being disclosed to any person not a member of the board. Makes board records immune from legal process and inadmissible as evidence. (Sec. 548) Directs the Secretary to report to the defense committees on the number of military personnel who, during the period beginning on January 1, 2005, and ending on the date of enactment of this Act, have not received at least 30 days notice before a deployment that will last 180 days or more. Subtitle E: Military Justice Matters - (Sec. 551) Requires the military department Secretaries to amend current or prescribe new regulations to subject military personnel who are ordered to active duty at locations overseas in an inactive duty for training status to the jurisdiction of the Uniform Code of Military Justice (UCMJ) continuously from commencement to conclusion of such orders. (Sec. 552) Applies UCMJ provisions to declared wars or contingency operations (currently, only "war"). Subtitle F: Decorations and Awards - (Sec. 555) Authorizes the presentation of a Medal of Honor flag to living Medal recipients or to the living next of kin of deceased Medal recipients. (Sec. 556) Directs the President to report to the defense committees on the advisability of modifying the criteria for the award of the Purple Heart to authorize its award to members who die in captivity under unknown circumstances or as a result of conditions or treatment which currently do not qualify the decedent for the Purple Heart, and for members who survive captivity as prisoners of war, but die thereafter as a result of a disease or disability incurred during such captivity. (Sec. 557) Requires the Secretary to: (1) review the policy, procedures, and processes of the military departments for awarding decorations to members of the Armed Forces; and (2) report review results to the defense committees. Subtitle G: Matters Relating to Casualties - (Sec. 561) Authorizes severely injured or ill members who have been provided assistive technology or devices to retain such technology or devices after separation from service. (Sec. 562) Directs the Secretary concerned to provide transportation of the remains of a member who dies in a combat theater of operations and whose remains are returned to the United States through the mortuary facility at Dover Air Force Base, Delaware. Requires a military escort to travel with the remains. (Sec. 563) Directs the Secretary to submit to Congress, as part of the annual defense budget request for a fiscal year, a consolidated budget justification display, in classified and unclassified form, that covers all programs and activities of DOD POW/MIA accounting and recovery organizations. (Sec. 564) Directs the Secretary to establish within DOD a center to augment and support programs and activities of the military departments for the provision of assistance to severely wounded or injured servicemembers. Designates such center as the Military Severely Injured Center. Requires the Center to establish a database for tracking severely wounded or injured servicemembers. (Sec. 565) Requires the Secretary, as soon as practicable after the completion of the comprehensive review of DOD procedures on mortuary affairs, to report to the defense committees on such review. (Sec. 566) Amends the NDAA for Fiscal Year 2006 to require an additional element in the DOD policy of casualty assistance to survivors of military decedents. (Sec. 567) Requires the Secretary concerned to ensure that each military health care professional within that department who is deployed to a theater of combat operations is trained, before such deployment, in the preservation of remains under combat or combat-related conditions. Subtitle H: Impact Aid and Defense Dependents Education System - (Sec. 571) Amends the Defense Dependents' Education Act of 1978 to allow the enrollment in the defense dependents' education system of children of a foreign military member assigned to the Supreme Headquarters Allied Powers, Europe, in a school of the defense dependents' education system in Mons, Belgium, through the 2010-2011 school year. Requires a report from the Secretary to Congress evaluating alternatives for the education of U.S. military dependents and dependents of foreign military personnel assigned to such Headquarters. (Sec. 572) Earmarks specified defense-wide O&M funds for providing assistance to local educational agencies (LEAs) that have military dependent students comprising at least 20% of the students in average daily attendance during a year. Provides further assistance to Leas that experience significant increases or decreases in average daily attendance of military dependent students due to military force structure changes, the relocation of military forces from one base to another, and base closures and realignments. (Sec. 573) Earmarks specified defense-wide O&M funds for impact aid payments for children with disabilities as authorized under the Elementary and Secondary Education Act of 1965. (Sec. 574) Requires a report from the Secretary to the defense and appropriations committees on a plan to provide assistance to Leas that experience growth in the enrollment of military dependent students as a result of force structure changes, the relocation of a military unit, or the closure or realignment of a military installation pursuant to a defense base closure law. Requires annual plan updates. Directs the Secretary, from the date of enactment of this Act through September 30, 2011, to work collaboratively with the Secretary of Education to ease the transition of military dependent students from attendance in DOD dependent schools to attendance in schools of Leas (Sec. 575) Directs the Secretary to carry out a three-year pilot program on the provision of educational and support tools to promote early childhood education for dependent children affected by a military deployment or the relocation of a military unit. Requires a program report from the Secretary to the defense committees. Subtitle I: Armed Forces Retirement Home - (Sec. 578) Requires a report from the Secretary to the defense and appropriations committees with respect to leadership and management of the Armed Forces Retirement Home, including the effect of changing the title of the Chief Operating Officer of the Home and the need for a greater role by active-duty military personnel in overall Home direction, operation, and management. (Sec. 579) Directs the Secretary to report to the defense and appropriations committees on the composition and activities of local boards of trustees of the Home. Subtitle J: Reports - (Sec. 581) Directs the Secretary to report to the defense committees on personnel requirements for airborne assets identified as low-density, high-demand airborne assets based on combatant commander requirements to conduct and sustain operations for the global war on terrorism. (Sec. 582) Directs the Secretary to: (1) review the feasibility and cost-effectiveness of establishing on Guam a station to process new U.S. military recruits drawn from the western Pacific region; and (2) report review results to the defense committees. (Sec. 583) Amends the Reagan Act to include within a required annual report on sexual assaults in the military the results of any disciplinary actions taken. (Sec. 584) Requires a report from the Secretary to the defense and appropriations committees on the feasibility and advisability of providing an electronic copy of military records to members upon their discharge or release from service. (Sec. 585) Directs the Secretary to report to Congress on the feasibility of using military identification cards that do not contain, display, or exhibit the individual's Social Security number. (Sec. 586) Directs the Secretary to report to the defense committees on how the data contained in the DOD Joint Advertising, Market Research, and Studies program is maintained and protected. (Sec. 587) Directs the CG to report to Congress concerning members of the Armed Forces claiming status as military conscientious objector between September 11, 2001, and December 31, 2006. Subtitle K: Other Matters - (Sec. 591) Reduces DOD's accrual contributions into the Department of Defense Military Retirement Fund by requiring the military department concerned to contribute at the lower, part-time rate for reserve personnel who are mobilized or serving on active duty for special work. (Sec. 592) Revises the formula by which government contributions are made to the Medicare-Eligible Uniformed Services Retiree Health Care Fund (for the financing of health care for military retirees who are also eligible for health care under Medicare). Excludes, for purposes of the formula: (1) cadets and midshipmen at service academies; and (2) certain reserve personnel who are not counted against active-duty end strengths. Bases reserve personnel numbers on the number of members of the Selected Reserve (smaller) rather than the Ready Reserve. (Sec. 593) Renames the Navy's Dental Division as the Dental Corps, under the direction of the Chief of the Dental Corps. (Sec. 594) Makes permanent (currently, ends December 31, 2007) DOD authority to expend appropriated funds to present recognition items for military recruitment and retention purposes. (Sec. 595) Allows the Secretary to designate a person to administer a military enlistment or appointment oath. (Sec. 596) Repeals the requirement of periodic DOD Inspector General assessments of military installation compliance with requirements of the Uniformed and Overseas Citizens Absentee Voting Rights Act. Requires a report from the CG to Congress on DOD programs and activities to facilitate voter registration and voting, including Internet-based electronic voting. Directs the Secretary to continue the Interim Voting Assistance System ballot request program with respect to all absent military voters, overseas DOD employees, and their dependents for all elections through December 31, 2006. Requires reports from the Secretary to Congress on: (1) assessments and recommendations with respect to the Interim Voting Assistance System; and (2) plans for expanding the use of electronic voting technology for individuals covered under the Uniformed Overseas Citizens Absentee Voting Act for elections through November 30, 2010. (Sec. 597) Directs each military department Secretary to ensure, in the case of any member of the Armed Forces appearing before a physical evaluation board, that the board's decision conveys findings and conclusions with specific attention to each issue provided by the member in regard to that case. Requires the presence of physical evaluation board liaison officers to provide advice, counsel, and general information to such members on the operation of such boards. Requires the Secretary of Defense to assess military department compliance with such requirements, as well as with standards and guidelines for board training and staff, at least every three years. (Sec. 598) Requires the Secretary concerned to issue a permanent military ID card to a permanently disabled dependent of a military retiree. (Sec. 599) Outlines the composition of the United States Drum and Bugle Corps. Authorizes the President to appoint members of that Corps and the United States Marine Band to grades not above captain. Provides for the retirement of members of both groups. Title VI: Compensation and Other Personnel Benefits - Subtitle A: Pay and Allowances - (Sec. 601) Waives any FY2007 pay increases tied to increases in the General Schedule of Compensation for government employees. Increases, effective January 1, 2007, by 2.2% the rates of basic pay for military personnel. Revises, effective April 1, 2007, the rates of basic pay within each pay grade for commissioned officers, warrant officers, and enlisted personnel. (Sec. 602) Increases maximum pay levels for general and flag officers to reflect increases in maximum salaries for Senior Executive Service personnel. (Sec. 603) Extends through December 31, 2007, the prohibition against requiring certain injured military personnel to pay for meals provided by military treatment facilities. (Sec. 604) Authorizes the Secretary concerned, as of October 1, 2006, to provide a second basic allowance for housing (BAH) to reserve members without dependents mobilized in support of a contingency operation and serving in a location that does not allow the member to reside at their permanent residence. (Sec. 605) Authorizes the spouse of a member who dies while serving on active duty to receive a BAH for up to 365 days after the date of the member's death, even though the spouse is also a member of the Armed Forces. (Sec. 606) Requires the Secretary concerned to pay the full premium (currently, only the premium required for the first $150,000 worth of coverage ) for coverage under the Servicemembers' Group Life Insurance (SGLI) program for members serving in Operations Enduring Freedom or Iraqi Freedom. (Sec. 607) States that the prohibition barring reserve personnel from receiving compensation for work or study performed in a correspondence course shall apply to any work or study performed on or after September 7, 1962, and includes members of the National Guard while not in federal service. (Sec. 608) Amends the NDAA for Fiscal Year 2006 to extend through 2008 a pilot program on contributions to the Thrift Savings Plan (TSP) for initial Army enlistees. Subtitle B: Bonuses and Special and Incentive Pays - (Sec. 611) Extends through 2007 specified authorities currently scheduled to expire at the end of 2006 with respect to certain special pay and bonus programs within the regular and reserve Armed Forces. (Sec. 615) Allows military dentists to be paid additional special pay while also receiving variable special pay for participation in internship or residency programs. (Sec. 616) Increases from $10,000 to $25,000 the maximum annual special pay for Selected Reserve health care professionals serving in critically short wartime specialties. (Sec. 617) Increases from $30,000 to $200,000 the maximum bonus for dental officers. Authorizes a bonus payment of up to $400,000 to a person who is a graduate of an accredited school of medicine or osteopathy in a specialty designated by DOD as a critically short wartime specialty and who executes a written agreement to accept a commission as a medical officer in the Armed Forces and remain on active duty for at least four consecutive years. Requires pro rata repayment for time not successfully served. Terminates the bonus program on December 31, 2007. (Sec. 618) Allows the payment of nuclear officer incentive pay as a lump sum or in variable annual amounts in addition to payment in equal annual installments. (Sec. 619) Increases from: (1) $20,000 to $30,000 the maximum nuclear career accession bonus; and (2) $2,500 to $10,000 the maximum incentive bonus for transfer between the Armed Forces due to a shortage of trained and qualified personnel. (Sec. 621) Authorizes the Secretary to pay a bonus to a retired member of the regular or reserve Armed Forces who executes an agreement to serve on active duty in an assignment intended to alleviate a high-demand, low-density military capability or in any other specialty designated as critical to meet wartime or peacetime requirements. Limits the bonus to $50,000. Authorizes the Secretary to develop and provide additional incentives to encourage such members to return to active duty in such assignments. Requires the Secretary to report to the defense and appropriations committees describing such incentives at least 30 days before offering the incentives. Requires bonus repayment by members failing to serve the agreed-upon period. Terminates the program after December 31, 2010. Authorizes the Secretary of a military department to order to active duty a member who agrees to such an assignment, with the same deadline date. Limits to $5 million the FY2007 obligations that may be incurred for the bonus program. (Sec. 622) Authorizes an accession bonus of up to $8,000 for a person who, by December 31, 2007, executes a written agreement to complete officer candidate school, accept a commission as an officer, and serve on active duty for a period specified in the agreement. Requires repayment for unserved periods. Authorizes the Secretary of the Army to provide such a bonus to a person who, during the period beginning on April 1, 2005, and ending on April 1, 2006, executed an agreement to enlist for the purpose of attending officer candidate school. (Sec. 623) Revises provisions concerning the targeted shaping of the Armed Forces to: (1) make the voluntary separation incentive (VSI) available to officers and enlisted personnel with more than six but not more than 20 years of service; (2) increase the maximum VSI to no greater than four times the full amount of separation pay for a member of the same pay grade and years of service who is involuntarily separated; (3) extend through 2012 the authority to make VSI payments; and (4) provide, during the period beginning on October 1, 2006, and ending on December 31, 2012, enhanced authority for selective early retirement and early discharges. (Sec. 624) Amends the NDAA for Fiscal Year 2006 to include, under a bonus payment program for referring other persons for enlistment into the Army: (1) members of a reserve component under 60 years of age who, but for such age, would be eligible for military retired pay: and (2) civilian Army employees. Makes ineligible for such bonus JROTC administrators or instructors or retired Army members employed as JROTC administrators or instructors. Increases from $1,000 to $2,000 the maximum bonus amount, payable in two equal installments at the beginning and completion of basic training of the individual referred. Subtitle C: Travel and Transportation Allowances - (Sec. 631) Includes family members who are also military members under the authority to pay for the travel and transportation of family members to visit ill or injured military personnel. Subtitle D: Retired Pay and Survivor Benefits - (Sec. 641) Requires the determination of the retired pay base of general and flag officers (pay grades O-7 through O-10) to be based on rates of basic pay provided by law, without taking into account any pre-retirement reduction in such pay due to comparability with Executive Schedule pay. (Sec. 642) Revises the retired pay multiplier maximum percentage with respect to members retiring with more than 30 years of creditable military service. (Sec. 643) Authorizes a participant in the Survivor Benefit Plan (SBP), in the case of the death of the chosen beneficiary, to elect a new beneficiary within 180 days after the death of the previous beneficiary. Outlines provisions concerning the change in premium after election of the new beneficiary. (Sec. 644) Makes members who die after October 7, 2001 (currently, November 23, 2003) eligible to choose optional annuities for dependents under the SBP. (Sec. 645) Directs the Secretary to report to the defense committees on factors that affect retention of members who have a special operations forces designation. Subtitle E: Commissary and Nonappropriated Fund Instrumentality Benefits - (Sec. 661) States that, for products sold at commissary or exchange stores at a surcharge above the normal five-percent-over-cost (items such as tobacco products, disposable cameras, film, and telephone calling cards), the surcharge shall be applied to the surcharge fund as if it were a uniform surcharge product. (Sec. 662) Requires lessees of non-excess DOD property to provide military exchanges, commissaries, and morale, welfare, and recreation activities (covered entities) the right to establish and operate a community support facility, provide community support services, or seek equitable compensation for DOD morale, welfare, and recreation programs in lieu of the operation of such a facility or the provision of such services, if the Secretary determines that the lessee will provide merchandise or services in direct competition with the covered entities. Requires a covered entity to exercise such right within 90 days after notification from the Secretary of its opportunity to do so. Allows the Secretary concerned to waive such right in the best interests of the United States. Directs the Secretary concerned to notify the defense committees of all leases that include the operation of a community support facility or the provision of community support services. (Sec. 663) Requires a report from the Secretary to Congress on the cost-effectiveness of purchasing commercial insurance for commissary and exchange facilities and facilities of other morale, welfare, and recreation programs and nonappropriated fund instrumentalities. (Sec. 664) Directs the Secretary to conduct a study regarding the capability of morale, welfare, and recreation facilities and activities operated by a DOD nonappropriated fund instrumentality to provide access to and accommodate disabled persons who are otherwise eligible to use such facilities or participate in such activities, as well as the legal requirements with respect to such access and accommodation as outlined under the Rehabilitation Act of 1973. Requires the Secretary to report study results to Congress. Subtitle F: Other Matters - (Sec. 670) Establishes additional protections for servicemembers and their dependents who are extended credit. Prohibits a creditor from charging an annual interest rate greater than 36% with respect to such members and dependents. Outlines mandatory loan disclosures. Preempts inconsistent state law. Provides prohibited creditor practices, as well as penalties and remedies for violations. (Sec. 671) Includes claims of up to $10,000 (currently $1,500) within the authority of the Secretary concerned to waive claims against members for erroneous overpayment of pay and allowances. Increases from three to five years after such overpayment the time period during which a member's application for such waiver will be accepted. (Sec. 672) Prohibits DOD from notifying consumer reporting agencies regarding debts of or erroneous payments made to a member while a decision is pending regarding the waiver, remission, or cancellation of such debt or payment, unless the Secretary concerned determines that such disclosure is in the best interests of the United States. Requires a report from the Secretary to the defense and appropriations committees on the exercise of such authority. (Sec. 673) Includes a retired or former member of a military department (currently, only a member on active duty, or a reserve member in an active status) within provisions authorizing the Secretary to remit or cancel the indebtedness of members. Removes time limits on the exercise of such authority (instead requiring the Secretary to prescribe regulations). (Sec. 674) Provides for: (1) the repayment in monthly installments, by a member to the United States, of any indebtedness owed by the member due to the overpayment of military pay or allowances made through no fault of the member; and (2) a 90-day delay in the recovery of any such overpayment with respect to members injured in the line of duty or incurring a wound, injury, or illness in a combat operation or combat zone. (Sec. 675) Directs the Secretary to carry out, in at least six regions of the country, a joint family support assistance program for families of members of the Armed Forces. Directs the Secretary to submit to the defense and appropriations committees: (1) a plan for program implementation; and (2) a program report after plan implementation. Terminates the program three years after the first obligation of program funds. (Sec. 676) Directs the Secretary to establish within DOD a working group to identify and assess the needs of members of the National Guard and Reserve returning from deployment in Operations Iraqi Freedom or Enduring Freedom in transitioning to civilian employment. Requires: (1) an activities report from the working group to the Secretary and Congress; and (2) such report to be made available to the public. Terminates the working group two years after the date of enactment of this Act. (Sec. 677) Requires the Secretary of the Army to: (1) conduct an audit of the pay accounts of each Army member wounded or injured in a combat zone who was evacuated for inpatient care during the period beginning on May 1, 2005, and ending on April 30, 2006; and (2) report to the defense and appropriations committees on audit results. (Sec. 678) Requires a report from the Secretary of the Army to Congress on the number of individuals affected by a current inequity in the provision of assignment incentive pay to members of the Army National Guard and Army Reserve on active duty in Afghanistan and Iraq. (Sec. 679) Expresses the sense of Congress that there should be paid to each living Bataan Death March survivor, or to their unremarried surviving spouse, an appropriate amount of compensation in recognition of their captivity. Title VII: Health Care Provisions - Subtitle A: TRICARE Program Improvements - (Sec. 701) Provides coverage under TRICARE (a DOD managed care program) for forensic examinations following sexual assault or domestic violence. (Sec. 702) Authorizes TRICARE coverage for anesthesia services and costs in connection with dental treatment for patients with developmental, mental, or physical disabilities, and for children under five years of age. (Sec. 703) Updates terms related to TRICARE primary and preventive health care services for women to include cervical and breast cancer screening. (Sec. 704) Prohibits DOD from increasing the premium, deductible, copayment, or other charge for TRICARE Prime, the charge of inpatient care for TRICARE Standard, and the premium for TRICARE Reserve Select and TRICARE Standard for members of the Selected Reserve and the Ready Reserve during the period from April 1, 2006, to December 31, 2007. (Sec. 705) Directs the Secretary to conduct a demonstration project to allow particular over-the-counter medications to be included on the DOD uniform formulary (in lieu of equivalent prescription drugs). Requires a project report from the Secretary to the defense committees. (Sec. 706) Provides TRICARE Standard coverage to members of the Selected Reserve and their families while such members are in a non-active duty status. (Sec. 707) Extends to the TRICARE program the same rule applicable under the Medicare program that prohibits an employer or other entity from offering any financial or other incentive for a TRICARE retired beneficiary not to enroll (or to terminate enrollment) under a group health plan which would be the primary payer to TRICARE. Makes such requirement inapplicable to employers with fewer than 20 employees. (Sec. 708) Provides copayment limits, for the period beginning on October 1, 2006, and ending on September 31, 2007, for the receipt of generic, formulary, and nonformulary agents under the retail pharmacy system of the DOD pharmacy benefits program. Directs the Secretary to transfer a specified amount from the National Defense Stockpile Transaction Fund to the Department of Defense Medicare-Eligible Retiree Health Care Fund. Subtitle B: Studies and Reports - (Sec. 711) Directs the Secretary to establish within DOD a task force to: (1) examine matters relating to the future of military health care; (2) report to the Secretary an assessment of, and recommendations for, sustaining the military health care services being provided to members of the Armed Forces, retirees, and their families; and (3) submit an interim and final report to the Secretary on its activities. Terminates the task force 90 days after the final report. (Sec. 712) Requires the Secretary to: (1) conduct a study of providing chiropractic health care services to members on active duty and their dependents, members of the Selected Reserve and their dependents, and members entitled to military retired pay and their dependents; and (2) report to the defense committees on study results. (Sec. 713) Requires the CG to conduct audits of: (1) the DOD initiative to manage future medical benefits, known as "Sustain the Benefit;" and (2) DOD costs in implementing the TRICARE Reserve Select Program. Directs the CG to report to the defense and appropriations committees on results of both audits. (Sec. 714) Provides for the transfer to the Medical Follow-up Agency of the Institute of Medicine of the National Academy of Sciences of data and biological specimens related to a current Air Force Health Study. Requires a report from the Secretary of the Air Force to the defense committees on such transfer. (Sec. 715) Requires the Secretary to study and report to the defense committees on the feasibility of allowing family members of reserve personnel who are called or ordered to active duty in support of a contingency operation to continue health care coverage under a civilian health care program and to provide reimbursement for such health care. (Sec. 716) Directs the Secretary to study and report to Congress on the health effects of exposure to depleted uranium munitions on uranium-exposed soldiers and on children of such soldiers who were born after the soldiers were so exposed. (Sec. 717) Requires the Secretary to: (1) develop a plan to provide services to military dependent children with autism pursuant to the DOD extended health care services program; and (2) report to the defense committees on the plan. (Sec. 718) Directs the CG to: (1) conduct a study of the DOD pharmacy benefits program; and (2) report study results to the defense and appropriations committees. (Sec. 719) Requires a report from the Secretary to the defense committees on actions taken in response to recommendations of the July 2001 report of the Department of Defense Healthcare Quality Initiatives Review Panel. Directs the Secretary to contract for an independent review of the DOD medical quality improvement program, and requires a report from the Secretary to such committees on the independent review. (Sec. 720) Directs the Secretary to report to the defense and appropriations committees on the distribution of hemostatic agents for members of the Armed Forces serving in Iraq and Afghanistan, including a description of any distribution problems and attempts to resolve such problems. (Sec. 721) Directs the Secretary to: (1) conduct a 15-year longitudinal study on the effects of traumatic brain injury incurred by members of the Armed Forces in Operations Iraqi Freedom and Enduring Freedom; and (2) provide periodic and final reports to Congress on study results. Subtitle C: Planning, Programming, and Management - (Sec. 731) Requires, effective as of the next contract option period for managed care support contracts under TRICARE, the standardization of claims processing under the TRICARE program with such processing under the Medicare program. Requires: (1) a report from the Secretary to the defense and appropriations committees on the collection of amounts owed to the United States from third party payers; and (2) annual reports from the Secretary to such committees on TRICARE claims processing requirements that differ from equivalent Medicare requirements. (Sec. 732) Requires: (1) TRICARE regional directors to annually develop integrated, comprehensive requirements for the support of military treatment facilities in that region that is provided by contract civilian health care and administrative personnel under the TRICARE program; (2) the Secretary to facilitate and enhance the support of such facilities in order to assure maximum quality and productivity; and (3) annual reports from the Secretary to the defense committees on the support provided. (Sec. 733) Directs the Secretary to: (1) report to the defense committees on uniform standards for the access of wounded, injured, or ill members of the Armed Forces to health care services in the United States following return from a combat zone; (2) require that health care services and rehabilitative needs of such members be met through whatever means possible, including referral to health care providers outside the military health care system; (3) establish and submit to the defense committees a uniform system for tracking the performance of the military health care system in meeting such needs; and (4) report quarterly during FY2007 to such committees on the military health care system's performance in meeting such needs. (Sec. 734) Requires the Secretary to: (1) design and develop a fully integrated program on disease and chronic care management for the military health care system that provides uniform policies and practices throughout such system, including both military hospitals and clinics and civilian health care providers within the TRICARE network; (2) develop an implementation plan for such program; and (3) report to the defense committees on the design, development, and implementation of the program. (Sec. 735) Amends the NDAA for Fiscal Year 2006 to require the task force on mental health established under such Act to consider, as part of its assessment of DOD mental health services provided to military personnel, the specific needs of members deployed in Operations Iraqi Freedom or Enduring Freedom upon their return from deployment. (Sec. 736) Authorizes the Secretary to extend for up to two additional one-year periods current TRICARE contracts for the delivery of health care, if the Secretary determines that such extension is in the best interests of the United States, is cost-effective, and will facilitate the effective administration of the TRICARE program and ensure continuity in the delivery of health care. Requires, before any such extension, 30 days' prior notification to the defense committees. Directs the Secretary to report to such committees on contracting mechanisms for future contracts for health care services support. (Sec. 737) Amends the NDAA for Fiscal Year 2006 to include, in a required study and report by the CG, the feasibility and advisability of transferring direct responsibility for DOD Vaccine Healthcare Centers from the Army Medical Command to the Under Secretary of Defense for Personnel and Readiness and the Assistant Secretary of Defense for Force Protection and Readiness. Prohibits the Secretary from downsizing or otherwise restructuring current Centers during FY2007. Requires the Secretary to ensure that military department Secretaries fund and maintain Centers of their departments. (Sec. 738) Requires additional elements for pre-deployment and post-deployment medical examinations, including current treatment and an assessment of traumatic brain injury. Provides criteria for referral for further evaluation. Directs the Secretary to prescribe minimum mental health standards for eligibility of a member for deployment to a combat or contingency operation. Requires the: (1) CG to conduct a study of, and report to the defense committees on, the implementation of the requirements of this section; and (2) the Secretary to implement the requirements and report to such committees on such implementation. Subtitle D: Other Matters - (Sec. 741) Directs the Secretary to carry out no less than three one-year pilot projects to evaluate the efficacy of various approaches to improving the capability of the military and civilian health care system to provide early diagnosis and treatment of post-traumatic stress disorder (PTSD) and other mental health conditions. Requires one of such projects to be: (1) designed to evaluate diagnostic and treatment approaches for use by primary care providers to improve the diagnosis and treatment of PTSD; (2) focused on members of the National Guard or Reserve located more than 40 miles from a military medical facility and whose personnel are served primarily by civilian community health resources; and (3) designed to provide outreach to family members on PTSD and other mental health conditions. Requires the Secretary to: (1) evaluate each project; and (2) report on each project to the defense and appropriations committees. (Sec. 742) Prohibits the Secretary concerned from converting any military medical or dental position to a civilian medical or dental position in a fiscal year unless such Secretary certifies to the defense and appropriations committees that such conversion will not increase cost or decrease quality of care or access to care. Directs: (1) the CG to report to such committees on a review of any such certifications; (2) each department Secretary to resubmit for FY2007 the related certification and report requirements under the NDAA for Fiscal Year 2006; and (3) the Secretary to report to the defense committees on any such conversions scheduled for FY2008. (Sec. 743) Extends through FY2010 the joint incentives program on the sharing of health care resources by DOD and the Department of Veterans Affairs. (Sec. 744) Requires the Secretary to establish within DOD a panel to develop curricula for training family members in the provision of care and assistance to members and former members with traumatic brain injuries. Designates such panel as the Traumatic Brain Injury Family Caregiver Panel. Requires: (1) dissemination of the curricula developed; and (2) a report from the Secretary and the Secretary of Veterans Affairs to the defense and veterans' committees on actions taken with respect to such curricula. (Sec. 745) Recognizes and commends Representative Lane Evans for his 24 years of service to benefit the people of Illinois, members of the Armed Forces and their families, veterans, and the United States. Title VIII: Acquisition Policy, Acquisition Management, and Related Matters - Subtitle A: Provisions Relating to Major Defense Acquisition Programs - (Sec. 801) Directs the Under Secretary to: (1) develop a training program to certify civilian and military personnel of DOD with responsibility for generating requirements for major defense acquisition programs (MDAPs); and (2) establish competency requirements for personnel undergoing the training program. Requires reports, in 2007 and 2008, from the Secretary to the defense committees on implementation of the training program. (Sec. 802) Directs the Secretary to require program managers for major weapons systems and subsystems to assess the long-term technical data needs of such systems and subsystems and establish corresponding acquisition strategies needed to sustain such systems and subsystems over their life cycle. Requires that, in the case of a challenge to a use or release restriction of technical data of a contractor or subcontractor for a major system or subsystem on the basis that the system, subsystem, or component was developed exclusively at private expense, the burden of proof of such private development shall be on the contractor or subcontractor. (Sec. 803) Directs the Secretary to: (1) conduct a study on revisions to requirements relating to Selected Acquisition Reports; and (2) report to the defense committees on study results. (Sec. 804) Requires the Secretary to provide biannual updates to the defense committees on the implementation of plans to reform the DOD acquisition system. (Sec. 805) Requires, before an MDAP may proceed to Milestone B, certification that: (1) market research has been conducted prior to technology development to reduce duplication of existing technology and products; (2) reasonable cost and schedule estimates have been developed; and (3) funding is available to execute the product development and product production plan. (Sec. 806) Modifies the definition of "original baseline estimate" with respect to an MDAP to mean the baseline established before the program enters into system development and demonstration, or at program initiation, whichever occurs later. (Sec. 807) Prohibits an entity performing lead system integrator functions in the acquisition of a major system by DOD from having any direct financial interest in the development or construction of any individual system or element thereof. Provides an exception in the case of certain certifications made by the Secretary to the defense committees with respect to such entity. Requires the Secretary to update DOD acquisition regulations with respect to lead system integrators as required under the NDAA for Fiscal Year 2006 and this section. Subtitle B: Acquisition Policy and Management - (Sec. 811) Prohibits the DOD executive or milestone decision authority entity for a DOD information technology business system that is not a national security system from providing Milestone A approval for the system unless, as part of the approval decision, the executive or authority determines that the system will achieve initial operational capability within five years of such approval. (Sec. 812) Directs the Secretary to carry out a pilot program on the use of time-certain development in the acquisition of major weapon systems. Limits to six the number of major weapon systems to be included in the program. Provides special funding authority, and requires reports from the Secretary to the defense and appropriations committees on the use of program funds. Prohibits a major weapon system from being included in the program after September 30, 2012. Requires an annual program report from the Secretary to such committees. (Sec. 813) Directs the Secretary to establish the Panel on Contracting Integrity to: (1) conduct reviews of DOD progress to eliminate areas of vulnerability of the defense contracting system that allow fraud, waste, and abuse; (2) review a required CG report relating to areas of vulnerability in DOD contracts; and (3) recommend changes in law and policy necessary to eliminate such areas of vulnerability. Requires annual reports from the Panel to the defense and appropriations committees. Terminates the panel on December 31, 2009. (Sec. 814) Requires the Secretary to: (1) issue guidance, with detailed implementation instructions, for DOD on the appropriate use of award and incentive fees in DOD acquisition programs; (2) select a federally funded research and development center to assess various mechanisms to ensure independent evaluation of contractor performance prior to making determinations on the judging and payment of award fees; and (3) report to the defense and appropriations committees on the assessment conducted under (2), above. (Sec. 815) Requires the Secretary to report to Congress on the application of the DOD Instruction entitled "Contractor Personnel Authorized to Accompany the United States Armed Forces." (Sec. 816) Adds new federal provisions concerning major automated information system programs. Defines a "major automated information system program" as a DOD program for the acquisition of an automated information system designated as a major automated information system, or of which the dollar value exceeds specified amounts (measured by costs in a single fiscal year, all program acquisition costs, or total life-cycle program costs). Allows adjustment of dollar values on the basis of DOD escalation rates. Directs the Secretary to submit to Congress each calendar year budget justification documents regarding cost, schedule, and performance for each major automated information system program for which funds are requested by the President in the budget. Requires quarterly reports from program managers and senior DOD officials responsible for a program, as well as reports on significant and critical changes in a program. Directs the Secretary to submit to the defense and appropriations committees the reporting requirements applicable to major automated information system programs, including those requirements considered to be duplicative or redundant. Makes this section effective as of January 1, 2008. (Sec. 817) Requires the DOD Inspector General and the inspectors general of the Department of Veterans Affairs and the National Institutes of Health (non-defense agencies) to: (1) review the procurement policies, procedures, and internal controls of such non-defense agency that are applicable to the procurement of property and services on behalf of DOD; and (2) determine whether such non-defense agency is in compliance with defense procurement requirements. Requires certain actions from the non-defense agency inspectors general following any determination other than compliance until such compliance is met. Directs the DOD Inspector General and the non-defense agency inspectors general to enter into a memorandum of understanding concerning the required reviews. Limits the amount of procurements, for the period after March 15, 2007, and before June 16, 2008, that may be made by DOD through a non-compliant non-defense agency. Allows an exception to such limitation when the Under Secretary determines it necessary to the interests of DOD to continue to procure property and services through such non-defense agency. Terminates the limitation upon non-defense agency compliance. (Sec. 818) Directs the Secretary to modify DOD regulations on the use of fixed-price type contracts in development programs. Authorizes the use of a different type of contract (such as a cost contract) upon certain determinations. (Sec. 819) Amends the Strom Thurmond NDAA for Fiscal Year 1999 to extend through 2009 required reports on DOD commercial price trend analyses. (Sec. 820) States as the goal of DOD and each of the military departments to ensure that, within five years after the date of enactment of this Act, for each MDAP and each major automated information system program, each of the following positions is performed by a properly qualified member of the Armed Forces or full-time DOD employee: program manager; deputy program manager; chief engineer; systems engineer; and cost estimator. Requires the Secretary to: (1) develop and begin implementation of a plan of action for recruiting and training appropriate military and civilian personnel to achieve such goal; and (2) report annually to the defense and appropriations committees on progress made toward such goal. Subtitle C: Amendments to General Contracting Authorities, Procedures, and Limitations - (Sec. 831) Amends the NDAA for Fiscal Year 2004 to extend through FY2007 the special temporary DOD authority to close out certain contracts entered prior to October 1, 1996. (Sec. 832) Prohibits the Secretary from entering into a service contract to acquire a military flight simulator unless the Secretary: (1) determines that a waiver is necessary for national security purposes; and (2) provides the defense and appropriations committees an economic analysis of of the need for such a contract at least 30 days before the waiver takes effect. (Sec. 833) Authorizes the Administrator of the General Services Administration (GSA) to allow state or local governments to use GSA federal supply schedules for goods and services to facilitate recovery from natural disasters, terrorism, or nuclear, biological, chemical, or radiological attack. (Sec. 834) Allows an executive agency to issue a waiver to extend a task order contract providing advisory or assistance services to DOD or another executive agency for up to ten additional years if the head of the agency determines in writing that: (1) the contract provides engineering or technical services so unique that award of a new contract would be harmful to the continuity of the program for which the services are performed; (2) award of a new contract would create a large disruption in services provided to DOD; and (3) DOD would endure program risk during critical program stages due to loss of corporate knowledge of ongoing program activities. Requires a report from the: (1) Secretary to the defense committees on advisory and assistance services; and (2) Administrator for Federal Procurement Policy to specified congressional committees on advisory and assistance services. Prohibits the issuance of any waiver under this section until the appropriate report is submitted. Terminates the waiver authority on December 31, 2011. Directs the CG to report to specified congressional committees on the use of advisory and assistance services contracts by the federal government. Subtitle D: United States Defense Industrial Base Provisions - (Sec. 841) Amends the NDAA for Fiscal Year 2004 to require, in an annual assessment and report of U.S. defense industrial base capabilities and acquisitions of articles, materials, and supplies manufactured outside the United States, information concerning: (1) the dollar value of all such articles, materials, and supplies purchased; and (2) all waivers granted with respect to such purchases under the Buy American Act. (Sec. 842) Prohibits funds appropriated or otherwise made available to DOD from being used for the procurement of a specialty metal if that metal or item is not melted or produced in the United States. Provides exceptions, including: (1) when satisfactory quality and sufficient quantity cannot be procured as and when needed; (2) procurements outside the United States in support of combat or contingency operations or other unusual and compelling urgency of need; and (3) when necessary to comply with trade agreements with foreign governments. Makes the prohibition inapplicable to: (1) items purchased for resale in commissaries, exchanges, and nonappropriated fund instrumentalities operated by DOD; (2) procurements in amounts not greater than the simplified acquisition threshold; and (3) procurements of commercially available electronic components whose specialty metal content is de minimis compared to its overall value. Authorizes a one-time waiver of the specialty metals domestic source requirement for specialty metals that were incorporated into items produced, manufactured, or assembled in the United States before the enactment of this Act, under certain conditions. Terminates the latter waiver authority at the end of FY2010. (Sec. 843) Requires the Secretary to establish a Strategic Materials Protection Board to, among other things: (1) determine the need to provide a long-term domestic supply of materials designated as critical to national security; (2) recommend a strategy to the President to ensure the domestic availability of designated critical materials; and (3) publish in the Federal Register, at least every two years, a list of designated materials, including critical specialty metals.. Subtitle E: Other Matters - (Sec. 851) Directs the CG to report to the defense committees on the employment of former DOD officials by major defense contractors during the most recent calendar year for which data are available. (Sec. 852) Requires the: (1) CG to issue a report on pass-through charges on contracts or subcontracts entered into for or on behalf of DOD; (2) Secretary to issue regulations to ensure that such charges are not excessive in relation to the cost of work performed; and (3) Secretary to report to the defense and appropriations committees on implementing such regulations. Applies such regulations to contracts or subcontracts awarded on or after May 1, 2007. (Sec. 853) Directs the Secretary to: (1) develop a comprehensive strategy for enhancing the role of DOD program managers in developing and carrying out defense acquisition programs; (2) revise DOD guidance for MDAPs to address the qualifications, responsibilities, tenure, and accountability of program managers for the MDAP program development and program execution periods; and (3) report to the defense and appropriations committees on such strategy and guidance. Requires the CG to report to such committees on actions taken by the Secretary. (Sec. 854) Requires the Secretary to: (1) develop joint policies for requirements definition, contingency program management, and contingency contracting during combat operations and post-conflict operations; and (2) submit an interim and final report to the defense committees on such definition, management, and contracting. (Sec. 855) Amends the NDAA for Fiscal Year 1994 to authorize the directors of the Defense Advanced Projects Agency and the Missile Defense Agency to carry out certain prototype projects in excess of $20 million but less than $100 million. (Sec. 856) Revises the application of the Randolph-Sheppard Act and the Javits-Wagner-O'Day Act (which require certain federal contracting with employers of persons with disabilities) to contracts and subcontracts for military dining support services and for general military dining facility operation. Directs the CG to review and report to the defense committees on DOD food service contracts entered into under both Acts. Requires the inspectors general of DOD and the Department of Education to jointly review, enter into a memorandum of understanding, and report to the defense committees on their respective management procedures under such Acts. (Sec. 857) Amends the Contract Disputes Act of 1978 to provide for the expedited disposition, by the Armed Forces Board of Contract Appeals and the Civilian Board of Contract Appeals, of appeals of small businesses where the amount in dispute is $150,000 or less. (Sec. 858) Includes Hispanic-serving institutions within DOD contracting goals for small disadvantaged businesses and certain institutions of higher education. Title IX: Department of Defense Organization and Management - Subtitle A: Department of Defense Management - (Sec. 901) Increases from nine to ten the authorized number of Assistant Secretaries of Defense. (Sec. 902) Expands the authorized activities under the Combatant Commanders Initiative Fund to include the provision of urgent and unanticipated humanitarian relief and reconstruction assistance, particularly in a foreign country where U.S. Armed Forces are engaged in a contingency operation. (Sec. 903) Adds the commander of the U.S. Strategic Command to the membership of the Nuclear Weapons Council. (Sec. 904) Consolidates the management of Department of Defense Regional Centers for Security Studies (currently operated under various authorities). Allows the Centers to pursue bilateral and multilateral research, communication, and exchange of ideas involving U.S. military and civilian personnel. Permits foreign governments and U.S. federal agencies to fund foreign participation in Center activities. Authorizes the Secretary to waive reimbursement of costs of activities for military officers and civilian defense and security officials from developing countries. Continues an annual reporting requirement from the Secretary to the defense committees on the operation of the Centers, with additional reporting requirements. (Sec. 905) Directs the Secretary to designate a senior acquisition official within the Office of the Under Secretary to oversee the exercise of acquisition authority by commanders of combatant commands and defense agency heads authorized to exercise acquisition authority. Requires such official to develop acquisition compliance guidance for use by such commanders and agency heads. (Sec. 906) Standardizes the definition of "national security system" within various laws applicable to DOD. (Sec. 907) Makes a technical change to reflect the current name of the Defense Information Systems Agency. Subtitle B: Space Activities - (Sec. 911) Amends the Commercial Space Transportation Competitiveness Act of 2000 to make conforming changes to reflect the organizational structure of the National Space-Based Positioning, Navigation, and Timing Executive Committee (which replaced the Interagency Global Positioning Executive Board). (Sec. 912) Extends through FY2009 the authority of the Secretary to conduct a pilot program of providing to non-U.S. government entities certain space surveillance data support. (Sec. 913) Directs the Secretary to establish within DOD the Operationally Responsive Space Program Office to contribute to the development of low-cost, rapid reaction payloads, spacelift, and launch control capabilities in order to fulfill joint military operational requirements for on-demand space support or reconstitution. Requires the Secretary to: (1) ensure that there is a separate DOD budget program element for operationally responsive space; and (2) submit to the defense and appropriations committees a plan for the DOD acquisition of capabilities for operationally responsive space to support military users and military operations. (Sec. 914) Directs the Secretary to select an independent entity to conduct a review and assessment of DOD organization and management for national security in space. Requires such entity to report review and assessment results to the Secretary and the defense and appropriations committees. Subtitle C: Chemical Demilitarization Program - (Sec. 921) Expresses the sense of Congress that: (1) the United States is committed to safely disposing its entire chemical weapons stockpile by the Chemical Weapons Convention deadline of April 29, 2012; (2) the Secretary should prepare a comprehensive schedule for safely destroying such weapons and preventing further delays in their destruction; (3) the Secretary should ensure adequate funding to complete the elimination of such stockpile in the shortest time possible; and (4) the Secretary should seek to gain the support of affected communities when selecting a site for the treatment or disposal of neutralized chemical agents. (Sec. 922) Directs the CG to submit to Congress a review of a cost-benefit analysis prepared by the Secretary of the Army concerning off-site versus on-site treatment and disposal of hydrolysate derived from the neutralization of VX nerve gas at the Newport Chemical Depot, Indiana. Limits the transportation of such materials pending such report. (Sec. 923) Authorizes the Secretary, in any contract for the destruction of the U.S. stockpile of lethal chemical agents and munitions pursuant to the Chemical Demilitarization Program under the Department of Defense Authorization Act, 1986, to provide the contractor an incentive to accelerate the safe elimination of the stockpile and to reduce the total cost of the Program by providing incentive payments for the early completion of destruction operations and the closure of the chemical demilitarization facility. Limits the amount of incentive payments. (Sec. 924) Authorizes the Secretary to carry out chemical demilitarization program responsibilities under the Department of Defense Authorization Act, 1986 through multiyear contracts entered into before the date of enactment of this Act. Subtitle D: Intelligence-Related Matters - (Sec. 931) Extends through 2010 DOD authority to engage in commercial activities as security (cover) for intelligence collection activities. (Sec. 932) Directs the Secretary to report annually to the defense, appropriations, and intelligence committees on DOD intelligence oversight activities. (Sec. 933) Amends the National Security Agency Act of 1959 to authorize the Director of the National Security Agency (NSA) to collect service charges for evaluating, certifying, or validating information assurance products under the National Information Assurance Program or its successor. Subtitle E: Other Matters - (Sec. 941) Requires the Secretary to: (1) develop a DOD-wide policy on RDT&E, procurement, and operation of unmanned systems; and (2) report the policy to the defense and appropriations committees. (Sec. 942) Provides an Executive Schedule Level IV (currently, Level III) pay grade for the position of Deputy Under Secretary of Defense for Logistics and Materiel Readiness. (Sec. 943) Directs the Secretary to: (1) submit to the defense and appropriations committees the results of an independent study of the Defense Travel System to determine the most cost-effective method of meeting DOD travel requirements; and (2) report to such committees on actions taken to implement such results. Prohibits a new contract or the expenditure of funds for such System until the report is submitted and implementation actions are taken. (Sec. 944) Transfers from the Director of National Intelligence to the Secretary administration of a pilot project on the establishment of a Civilian Linguist Reserve Corps under the Intelligence Authorization Act for Fiscal Year 2005. Directs the Secretary to carry out the pilot project through the National Security Education Program. Extends the pilot project for an additional two years. (Sec. 945) Revises the program of national security education scholarships, fellowships, and grants under the David L. Boren National Security Education Act of 1991 to modify the service agreement associated with participation in the National Security Education Program. Expands the entities at which required post-education service may be performed to include the Department of Homeland Security and the Department of State. Allows award recipients to fulfill their service requirement in a position in a discipline related to the study supported by the program, but only if no positions are available in federal agencies or offices covered under the program. Authorizes the Secretary to employ persons provided such assistance in a DOD position for up to two years following completion of their degree, if there is no other permanent position available for the participant. Requires the Secretary to submit to Congress a plan for improving the recruitment, placement, and retention within DOD of individuals who receive scholarships or fellowships under such Program. (Sec. 946) Directs the Secretary to report to the defense and appropriations committees assessing the posture of the U.S. Special Operations Command to conduct the global war on terrorism. Title X: General Provisions - Subtitle A: Financial Matters - (Sec. 1001) Authorizes the Secretary, in the national interest, to transfer up to $4.5 billion of the amounts made available to DOD in this Act between any such authorizations for that fiscal year, with limitations. Requires congressional notification of each transfer. (Sec. 1002) Adjusts amounts authorized to be appropriated to DOD in the NDAA for Fiscal Year 2006 by the amount by which appropriations pursuant to such authorizations are increased or decreased pursuant to titles I, II, and V of the Emergency Supplemental Appropriations Act for Defense, the Global War on Terror, and Hurricane Recovery, 2006. (Sec. 1003) Reduces by $757.051 million the total amount authorized to be appropriated in titles I through III of this Act, to be derived from savings resulting from lower-than-expected inflation. (Sec. 1004) Amends the NDAA for Fiscal Year 2006 to increase its FY2006 general transfer authority from $3.5 billion to $5 billion. (Sec. 1005) Provides the total amount to be contributed by the Secretary in FY2007 for the common-funded budgets of NATO (rather than the maximum amount otherwise applicable under the FY1998 baseline limitation). (Sec. 1006) Requires a report from the Secretary to the defense committees on the fuel rate and cost projection used in the annual DOD budget presentation. (Sec. 1007) Revises the annual due date of a required report on Office of Management and Budget (OMB) and Congressional Budget Office (CBO) outlay estimates. (Sec. 1008) Requires the President's annual budget to Congress for each fiscal year after 2007 to include specified budgeting for ongoing military operations in Afghanistan and Iraq. Subtitle B: Policy Relating to Vessels and Shipyards - (Sec. 1011) Reduces from 12 to 11 the minimum number of naval operational aircraft carriers. Prohibits the Secretary of the Navy from retiring the carrier U.S.S. John F. Kennedy from operational status until the Secretary of Defense makes certain certifications to the defense committees with respect to the need of such carrier by the Department of Homeland Security or NATO. Requires the Secretary of the Navy, if such carrier is retired, to maintain or ensure its maintenance to allow for reactivation in the event of a national emergency. (Sec. 1012) Expresses the sense of Congress that the nuclear-powered aircraft carrier designated CVN-78 should be named the U.S.S. Gerald R. Ford. (Sec. 1013) Authorizes the Secretary, in undertaking a vessel disposal or the disposal of a class of vessels, to dispose of another vessel or class of vessels if the substituted vessel(s) has (have) virtually identical capabilities. (Sec. 1014) Requires naval vessels homeported in Guam to be overhauled, repaired, or maintained in a shipyard in the United States or Guam. (Sec. 1015) Requires: (1) the Secretary of the Navy to report to the defense committees on future lease options available with respect to the Guam Shipyard; and (2) the CG to evaluate the report and report results to such committees. (Sec. 1016) Directs the Secretary of the Navy to conduct assessments of: (1) specified aspects of naval vessel construction to determine inefficiencies and design and production technologies that could address such inefficiencies; and (2) the effectiveness of the use in naval vessel construction contracts of special incentives for contractor investment in facilities and process improvement projects. Requires such Secretary to report to the defense and appropriations committees on such assessments. (Sec. 1017) Requires the Secretary to: (1) issue an acquisition policy that establishes, as a criterion in obtaining carriage by vessel of DOD cargo, the extent to which the offeror had overhaul, repair, and maintenance work for covered vessels performed in U.S. shipyards; (2) prescribe regulations to carry out such policy, and submit the regulations to the defense committees; and (3) report annually to such committees regarding overhaul, repair, and maintenance of covered vessels of offerors to which the policy applies. (Sec. 1018) Prohibits the Secretary from awarding any charter of a vessel for DOD, or contracting for the carriage of cargo by vessel for DOD, unless the charter or contract requires each riding gang (crew) member that performs work on the vessel during that period to follow federal transportation requirements for riding gang members, including U.S. citizenship or naturalization, work visa, and other documentation. Includes within such requirements that each such member hold a U.S.-issued merchant mariner's document. Allows exemptions by the Secretary with respect to individuals on a vessel for purposes other than vessel operation or maintenance, but requires a background check for each person so exempted who does not hold a merchant mariner's document. (Sec. 1019) Authorizes the President to transfer to Greece the ex-Liberty ship SS Arthur M. Huddell. Requires, as a transfer condition, that any necessary vessel repair or refurbishment be performed in a U.S. shipyard. Subtitle C: Counter-Drug Activities - (Sec. 1021) Amends the NDAA for Fiscal Year 1991 to extend through FY2011 DOD authority to assist the counterdrug activities of other federal departments or agencies, or of any state, local, or foreign law enforcement agency. (Sec. 1022) Extends through FY2008 DOD authority to support the counterdrug activities of other countries. Provides additional countries to which such support may be provided, and adds vehicles, aircraft, detection, and interception, monitoring, and testing equipment to the types of support that may be provided. Authorizes, in connection with such support but for the government of Afghanistan only, the provision of individual and crew-served weapons of .50 caliber or less and ammunition for counter-narcotics security forces. Increases the maximum annual amount of support for such program during FY2007 and FY2008. (Sec. 1023) Amends the Reagan Act to extend through FY2008 its authority to support a unified counterdrug and counterterrorism campaign in Colombia. (Sec. 1024) Amends the Spence Act to extend by two years a reporting requirement regarding DOD expenditures to support foreign counter-drug activities. Includes the foreign relations committees as report recipients. (Sec. 1025) Requires a report from the Secretary to the defense and appropriations committees updating the interagency counter-narcotics implementation plan for Afghanistan and specified countries of the South and Central Asian region. (Sec. 1026) Directs the Secretary, at least 30 days before implementing a decision to withdraw DOD helicopters from Operation Bahamas, Turks & Caicos (an operation to counter cocaine smuggling into the United States), to report to Congress the plan for the coordination of such Operation's mission, at the same level of effectiveness, using other U.S. government assets. Subtitle D: Force Structure and Defense Policy Matters - (Sec. 1031) Expresses the sense of Congress that the Quadrennial Defense Review (QDR) is intended to provide more than an overview of global threats and the general strategic orientation of DOD. Requires: (1) the QDR Board to make recommendations that are not constrained to comply with annual DOD budget reports submitted to Congress; and (2) QDR reports to include specific capabilities needed to achieve identified strategic and warfighting objectives, as well as homeland defense and support to civil authority missions of the active and reserve components. Directs the Secretary, at least six months before each QDR report is to be submitted to Congress, to establish a panel to conduct an independent assessment of such review. Requires the panel to report assessment results to the defense and appropriations committees. (Sec. 1032) Requires quarterly reports from the Secretary to the defense committees on the implementation of recommendations described in the 2006 QDR Report. (Sec. 1033) Directs the Secretary to report to the defense committees on the establishment of a U.S. Armed Forces regional combatant command for Africa. (Sec. 1034) Requires the Secretary to: (1) determine DOD intratheater and intertheater airlift and sealift mobility requirements; and (2) report such requirements to the defense and appropriations committees. (Sec. 1035) Directs the President to report to Congress on building interagency capacity and enhancing the integration of civilian capabilities of the executive branch with the capabilities of the Armed Forces to enhance the achievement of U.S. national security goals and objectives, including stability, security, transition, and reconstruction operations. Subtitle E: Reports - (Sec. 1041) Amends the NDAA for Fiscal Year 1994 to require an additional element concerning Defense Advanced Research Projects Agency (DARPA) research in a required annual report on chemical and biological warfare defense. (Sec. 1042) Directs the Secretary to: (1) conduct a study to determine DOD staffing and training requirements in support of national biosafety laboratories; and (2) report study results to the defense committees. (Sec. 1043) Requires the Secretary to report to the defense and appropriations committees on technologies that are being researched, developed, employed, or considered by the U.S. government or NATO for neutralizing or defeating threats to military rotary wing aircraft posed by portable air defense systems and rocket-propelled grenades. (Sec. 1044) Requires a report from: (1) the Secretary to specified congressional committees on DOD actions to develop standards for the testing and operation of unmanned aerial vehicles in the National Airspace System; and (2) the Administrator of the Federal Aviation Administration (FAA) to specified congressional committees on progress in developing a policy for testing and a plan for achieving wider access by such vehicles to operate in the System. (Sec. 1045) Requires a joint report from the Secretaries of Defense and Homeland Security to the defense, homeland security, and appropriations committees assessing the desirability and feasibility of offering incentives to members of the reserves, and former members of the Armed Forces within two years of separation from service, to encourage such members to serve in the Bureau of Customs and Border Protection. (Sec. 1046) Repeals specified reporting requirements under federal law and prior defense authorization Acts. (Sec. 1047) Directs the Secretary to report to the defense and appropriations committees on each report required of DOD under any provision of law enacted on or after the date of enactment of the NDAA for Fiscal Year 2004 and before February 1, 2007. Requires inclusion in such report of an assessment of the reporting burden imposed upon DOD, the utility of the report from the DOD perspective, and a recommendation on the advisability of repealing or modifying the report requirement. Subtitle F: Miscellaneous Authorities and Limitations on Availability and Use of Funds - (Sec. 1051) Authorizes the Secretary to accept reimbursement from non-federal sources to defray DOD costs from a conference, seminar, exhibition, symposium, or similar meeting conducted by DOD. Requires annual reports from the Secretary to the defense and appropriations committees summarizing the use of such authority. (Sec. 1052) Outlines the expenses for which the JCS Chairman may expend funds for joint staff exercises. (Sec. 1053) Prohibits a DOD officer or employee from directing the designation of funds for a particular purpose in the DOD defense budget with the knowledge or intent that such funds, if made available to DOD, will not be used for the designated purpose (parking of funds). Provides penalties. (Sec. 1054) Provides that, for purposes of discharging the duties of the Special Inspector General for Iraq Reconstruction, any funds appropriated or otherwise made available for FY2006 for the reconstruction of Iraq, regardless of their designation, shall be treated as amounts appropriated or otherwise made available for the Iraq Relief and Reconstruction Fund. Amends the Emergency Supplemental Appropriations Act for Defense and for the Reconstruction of Iraq and Afghanistan, 2004 to terminate the Office of the Inspector General on October 1, 2007, with transition operations authorized to continue through December 31, 2007. Subtitle G: Matters Involving Detainees - (Sec. 1061) Amends the Reagan Act to expand the information required in an annual report relating to investigations or prosecutions regarding the treatment of individuals detained by U.S. Armed Forces or by a person providing contract services to DOD. Subtitle H: Other Matters - (Sec. 1072) Amends the NDAA for Fiscal Year: (1) 2006 to extend a reporting and termination date for the Commission on the Implementation of the New Strategic Posture of the United States; and (2) 2001 to extend the due date for the final report of the Commission to Assess the Threat to the United States from Electromagnetic Pulse Attack. (Sec. 1074) Extends: (1) until the end of FY2007 the returning worker exemption under the Save Our Small and Seasonal Businesses Act of 2005. Repeals a prior sunset provision. (Sec. 1075) Extends until 14 years after the enactment of this Act the patent terms for badges of the American Legion, the American Legion Women's Auxiliary, and the Sons of the American Legion. (Sec. 1076) Revises federal provisions allowing the President to utilize the Armed Forces in connection with interference with federal and state law to allow the President to employ the Armed Forces and National Guard in federal service to restore public order in cases of natural disaster, epidemic or other public health emergency, terrorist attack or incident, or domestic violence. Requires the President to notify Congress within 14 days of the exercise of such authority. Authorizes the President, when exercising such authority, to direct the Secretary to provide supplies, services, and equipment to persons affected by the situation. (Sec. 1077) Directs the Secretary to ensure that current members of the Armed Forces, retired members, disabled veterans, and persons assisting disabled veterans are able to utilize lands under DOD jurisdiction that are available for hunting or fishing. Requires an assessment of such lands from the Secretary to Congress. Requires the Secretary of the Interior to immediately cease a plan to exterminate by helicopter the deer and elk on Santa Rosa Island, California. Title XI: Civilian Personnel Matters - (Sec. 1101) Authorizes the accrual of annual leave for members performing dual (military and civilian) employment. (Sec. 1102) Directs the Secretary to include in the Strategic Human Capital Plan required under the NDAA for Fiscal Year 2006 a strategic plan to shape and improve the senior management, functional, and technical workforce (including scientists and engineers) of DOD. (Sec. 1103) Amends the Strom Thurmond NDAA for Fiscal Year 1999 to extend through FY2011 a DOD experimental personnel management program for scientific and technical personnel. (Sec. 1104) Requires quarterly reports from the Secretary to the defense and appropriations committees on military personnel and DOD civilian employees who have served continuously in the Legislative Branch for more than 12 consecutive months in one or a combination of covered legislative details or fellowships. Requires that, if a member of the Armed Forces is assigned to a covered legislative detail or fellowship as his or her last tour of duty before retirement or separation in contravention of DOD regulations, then the Secretary shall report to the defense and appropriations committees on such assignment. (Sec. 1105) Amends the NDAA for Fiscal Year 2006 to extend through 2007 the authority to waive the annual limitation on total compensation paid to federal civilian employees working at an overseas location in an area of responsibility of the Central Command. Title XII: Matters Relating to Foreign Nations - Subtitle A: Assistance and Training - (Sec. 1201) Authorizes the Secretary, while conforming with all U.S. export control laws, to provide logistic support, supplies, and services to allied forces participating in a combined operation with U.S. Armed Forces. Limits to $100 million the total value of such support in a fiscal year. Requires an annual report from the Secretary to the defense and foreign relations committees on the use of such authority. (Sec. 1202) Authorizes the Secretary to use DOD acquisition and cross-servicing agreements to lend certain military equipment to foreign forces in Iraq and Afghanistan for personnel protection and survivability purposes. Limits the loan duration to one year. Directs the Secretary to submit semiannual reports to the defense and foreign relations committees on the use of such authority. Terminates such authority on September 30, 2008. (Sec. 1203) Codifies under federal Armed Forces law provisions relating to the DOD humanitarian demining assistance program. Authorizes the Secretary concerned to provide such assistance if it will promote either (currently, both): (1) the security interests of both the United States and the country in which the assistance is carried out; or (2) the specific operational readiness skills of military personnel participating in the program. Increases from $5 to $10 million the annual limit on the cost of equipment, services, and supplies under the program. (Sec. 1204) Renames the Regional Defense Counterterrorism Fellowship Program as the Regional Defense Combating Terrorism Fellowship Program. Increases from $20 million to $25 million the annual obligation limit under the Program. Allows the obligation of funds across fiscal years. (Sec. 1205) Allows the Secretary, during FY2007, to authorize the participation of members of the Armed Forces and civilian DOD personnel in multinational military centers of excellence hosted by any combination of the United States, any member nation of NATO, any major non-NATO ally, or any other friendly nation as identified by the Secretary for the purposes of: (1) enhancing the ability of military forces and civilian personnel to engage in joint exercises or coalition or international military operations; or (2) improving interoperability between the Armed Forces of the United States and the military forces of such foreign nation(s). Makes DOD O&M funds available for such purposes. Limits to $3 million the fiscal year funding limit for such participation, and allows DOD facilities and equipment to be used for the support of such centers. Requires a report from the Secretary to the defense committees on the use of such authority. (Sec. 1206) Amends provisions of the NDAA for Fiscal Year 2006 relating to DOD capacity-building of foreign military forces to allow the Secretary, with the concurrence of the Secretary of State , to authorize the commander of a combatant command to respond to unanticipated changes in a security environment within the commander's area of responsibility by conducting a program to build the capacity of the military forces of a foreign country within that commander's area of responsibility in order for such country to: (1) conduct counterterrorist operations; or (2) participate in or support military and stability operations. Provides an annual funding limit of $300 million. Requires congressional notification of the decision to support a capacity-building program in a foreign country. Terminates such authority at the end of FY2008. (Sec. 1207) Authorizes the Secretary to provide electronically-distributed learning content and associated information and technology for the education and training of military and civilian personnel of friendly foreign governments in order to enhance military interoperability between U.S. Armed Forces and military forces of such countries. Requires: (1) concurrence by the Secretary of State in the provision of such assistance; and (2) reports in 2007 and 2008 from the Secretary to the defense committees on the exercise of such authority. Terminates such authority at the end of FY2008. Subtitle B: Nonproliferation Matters and Countries of Concern - (Sec. 1211) Directs the President to appoint a senior presidential coordinator of U.S. policy on North Korea. Outlines coordinator duties. Requires a report from: (1) the coordinator to the President and Congress on actions taken; and (2) the President to Congress semiannually on the nuclear and missile programs of North Korea. (Sec. 1212) Requires a report from the Secretary to the defense and foreign relations committees on an increased role and participation of multinational partners in the United Nations Command in the Republic of Korea. (Sec. 1213) Requires the Director of National Intelligence to submit to Congress an updated National Intelligence Estimate on Iran. Requires a report from the President to Congress on U.S. policy on Iran. (Sec. 1214) Expresses the sense of Congress: (1) endorsing the policy of the United States to achieve a successful diplomatic outcome with respect to threats posed by the Iranian regime to acquire a capability to produce nuclear weapons; (2) calling on Iran to suspend its nuclear enrichment and reprocessing activities and achieve a negotiated outcome to concerns regarding its nuclear program; (3) urging the UN Security Council to work for the adoption of appropriate measures in the event Iran fails to comply with UN Security Council Resolution 1696; and (4) urging the President and Secretary of State to keep Congress fully informed on the progress of such diplomatic initiative. Subtitle C: Other Matters - (Sec. 1221) Excludes the acquisition of petroleum, oil, and lubricants from DOD limitations on the amount of liabilities that may be accrued under acquisition and cross-servicing agreements with foreign allies. Requires reports in 2007 and 2008 from the Secretary to the defense committees on the exercise of such authority. (Sec. 1222) Amends the American Servicemembers' Protection Act of 2002 to revise a definition of "United States military assistance" for purposes of such Act. (Sec. 1223) Expresses the sense of Congress that the Secretary should continue to provide space-available travel on military aircraft for humanitarian reasons to Iraqi children who would otherwise have no means to seek urgently needed medical care such as that provided by a humanitarian organization in Amman, Jordan. (Sec. 1224) Expresses the sense of Congress that the: (1) goal of the United States and its coalition partners has been to empower the Iraqi people and recognize their freedom to exercise full sovereignty and (2) government of Iraq should not grant amnesty to persons who have attacked, killed, or wounded members of the U.S. Armed Forces. (Sec. 1225) Requires annual reports through 2010 from the President to Congress listing all U.S. contributions to the UN and UN-affiliated agencies and related bodies. (Sec. 1226) Expresses the sense of Congress that the United States should: (1) support the establishment of a unified national government in Somalia, support humanitarian assistance to the people of Somalia, support efforts to prevent Somalia from being a safe haven for terrorists, and support regional stability there; (2) broaden and integrate its strategic approach toward Somalia within the context of other U.S. activities in the region; and (3) carry out all U.S. activities in Somalia within the framework of an interagency process. Directs the President to develop and submit to the defense and appropriations committees a comprehensive regional strategy toward Somalia within such context. Requires annual reports until 2010 from the President to the defense, foreign relations, and intelligence committees on strategy implementation. (Sec. 1227) Requires semiannual reports through 2011, from the Secretary to the defense and foreign relations committees, on implementation of the Darfur Peace Agreement of May 5, 2006, and DOD contributions to NATO in support of the African Union Mission in Sudan. (Sec. 1228) Expresses the sense of Congress that: (1) cooperation between the United States and Russia with regard to missile defense is in U.S. interests; (2) the United States should explore innovative and nontraditional means to achieve such cooperation; and (3) the Secretary should consider the possibility of such cooperation through the testing of detection and tracking equipment of the Missile Defense Agency through the use of Russian target missiles and the provision of early warning radar to the Agency by the use of Russian radar data. (Sec. 1229) Expresses the sense of Congress that the President should convene a summit as soon as possible for reaching a political agreement for Iraq that addresses fundamental issues regarding federalism, oil revenues, the militias, and economic recovery and reconstruction. (Sec. 1230) Expresses the sense of Congress commending U.S. Armed Forces, the intelligence community, other agencies, and coalition partners for actions taken that resulted in the death of Abu Musab al-Zarqawi, the leader of al-Qaeda in the Iraq terrorist organization and the most wanted terrorist in Iraq, as well as in other actions taken to ensure a free and prosperous Iraq. (Sec. 1231) Directs the Secretary to report annually to the defense and appropriations committees on foreign military sales and direct sales to foreign customers of significant military equipment manufactured in the United States. Title XIII: Cooperative Threat Reduction With States of the Former Soviet Union - (Sec. 1301) Specifies the cooperative threat reduction (CTR) programs to be funded through O&M funds provided under this Act. Makes funds appropriated for such purpose available for three years. Allocates such funds among specified CTR programs. Prohibits such funds from being used for purposes other than those specified until 30 days after the Secretary reports to Congress on the new purposes. Provides limited authority to vary allocated amounts in the national interest, after congressional notification. (Sec. 1303) Amends the Reagan Act to extend, until completion of the facility, the President's authority to waive certain funding restrictions during the construction of a chemical weapons destruction facility in Russia. Directs the Secretary to notify Congress of the date of completion. (Sec. 1304) Directs the Secretary to: (1) enter into an arrangement with the National Academy of Sciences under which the Academy carries out a study to identify areas for further cooperation with Russia and other states of the former Soviet Union under the CTR program in the specific area of biological weapons proliferation prevention; and (2) report study results to the defense committees. Title XIV: Matters Related to Defense Against Terrorism and Related Security Matters - (Sec. 1401) Revises DOD authority to pay monetary awards for assistance in combating terrorism to: (1) increase the maximum award from $2,500 to $10,000; and (2) delegate the authority to make such award, upon certain approval, to the commander of a command directly subordinate to the commander of a combatant command. (Sec. 1402) Directs the Secretary to report to Congress: (1) on the status of the threat posed by improvised explosive devices (IEDs) and efforts undertaken to defeat such threat; and (2) quarterly to Congress on incidents involving the detonation or discovery of an IED. Requires the quarterly reports to contain specified information regarding: (1) the Joint IED Defeat Organization and all other offices within DOD and the military departments that are focused on countering IEDs; (2) RDT&E of new countermeasures against such weapons; and (3) intelligence interdiction efforts against such weapons. (Sec. 1403) Directs the Secretary to ensure that by the end of FY2007 all U.S. military wheeled vehicles used in Iraq and Afghanistan outside of secure military operating bases are protected by IED jammers. Requires a report from the Secretary to the defense and appropriations committees on costs and timelines to complete such requirement. (Sec. 1404) Requires a report from the Secretary to the defense committees on the findings of a specified semiannual assessment process relating to the Global War on Terrorism. (Sec. 1405) States that confidential business information and other sensitive but unclassified homeland security information of DOD that is shared pursuant to the Homeland Security Act of 2006 with state and local personnel involved in the prevention, interdiction, or disruption of terrorist activity shall not be subject to public disclosure requirements of the Freedom of Information Act. (Sec. 1406) Directs the Secretary to ensure that a database containing specified emergency response and support capabilities is maintained by DOD. Title XV: Authorization for Increased Costs Due to Operation Iraqi Freedom and Operation Enduring Freedom - (Sec. 1501) Authorizes emergency supplemental appropriations to DOD for FY2007, for additional costs due to Operations Iraqi Freedom and Enduring Freedom, for: (1) procurement; (2) RDT&E; (3) O&M; (4) the Defense Health Program; (5) classified programs; (6) military personnel; (7) the Joint Improvised Explosive Device Defeat Fund; (8) the Iraq Freedom Fund; (9) the Iraq Security Forces Fund; and (10) the Afghanistan Security Forces Fund. Requires five days' prior notification of the defense and appropriations committees in the case of obligations or transfers from the funds described in (7) through (10), above. (Sec. 1512) Authorizes the Secretary, in the national interest, to transfer amounts made available in this title for FY2007 between any such authorizations for that fiscal year, with a total transfer limit of $ 2.5 billion. Requires prior transfer notification to the defense and appropriations committees. (Sec. 1518) Amends the NDAA for Fiscal Year 2006 to include the defense and appropriations committees as recipients of DOD supplemental and cost of war execution reports. (Sec. 1519) Prohibits the obligation or expenditure of funds authorized by this Act to: (1) establish a military installation or base for providing for the permanent stationing of U.S. Armed Forces in Iraq; or (2) exercise U.S. economic control over Iraq oil resources. (Sec. 1520) Authorizes supplemental appropriations for the Intelligence Community Management Account for FY2007. Division B: Military Construction Authorizations - Military Construction Authorization Act for Fiscal Year 2007 - (Sec. 2002) Recognizes Representative Joel Hefley for his 20 years of service to benefit the people of Colorado, members of the Armed Forces and their families, and the United States. Title XXI: Army - (Sec. 2101) Authorizes the Secretary of the Army to acquire real property and carry out military construction projects in specified amounts at specified installations and locations. Authorizes such Secretary to construct or acquire family housing units, carry out architectural planning and design activities, and improve existing military family housing in specified amounts. Authorizes appropriations to the Army for fiscal years after 2006 for military construction, land acquisition, and military family housing functions of the Army. Limits the total cost of construction projects authorized by this title. Title XXII: Navy - (Sec. 2201) Provides, with respect to the Navy, authorizations paralleling those provided for the Army under the previous title. (Sec. 2205) Amends the Military Construction Authorization Act (MCAA) for Fiscal Year 2004 and the MCAA for Fiscal Year 2005 to consolidate authority for the construction of an outlying landing field in Washington County, North Carolina. Amends the MCAA for Fiscal Year 2006 to revise a construction project for the Marine Corps Base, Camp Pendleton, California. Title XXIII: Air Force - (Sec. 2301) Provides, with respect to the Air Force, authorizations paralleling those provided for the Army under Title I of this Division. (Sec. 2305) Amends the MCAA for Fiscal Year 2006 to decrease the amount authorized for a construction project at MacDill Air Force Base, Florida. Title XXIV: Defense Agencies - (Sec. 2401) Authorizes the Secretary to acquire real property and carry out military construction projects in specified amounts at specified installations and locations. Authorizes the Secretary to construct or acquire family housing units, carry out architectural planning and design activities, and carry out certain energy conservation projects. (Sec. 2404) Authorizes the Secretary to carry out base closure and realignment activities, including real property acquisition and military construction projects, as authorized by the Defense Base Closure and Realignment Act of 1990 and funded through the Department of Defense Base Closure Account 2005. Amends the MCAA for Fiscal Year 2006 to authorizes the Secretary to carry out such activities under that Act. Limits the total cost of such activities under that Act. (Sec. 2405) Authorizes appropriations to DOD for fiscal years after 2006 for military construction, land acquisition, and military family housing functions of DOD. Limits the total cost of construction projects authorized by this title. (Sec. 2406) Amends the MCAA for Fiscal Year 2006 to increase the amounts authorized for a National Security Agency (NSA) construction project in Menwith Hall, United Kingdom. Title XXV: North Atlantic Treaty Organization Security Investment Program - (Sec. 2501) Authorizes the Secretary to make contributions for the North Atlantic Treaty Organization (NATO) Security Investment Program and authorizes appropriations for fiscal years after 2006 for such Program. Title XXVI: Guard and Reserve Forces Facilities - (Sec. 2601) Authorizes appropriations for fiscal years after 2006 for National Guard and reserve forces for acquisition, architectural and engineering services, and construction of facilities. Title XXVII: Expiration and Extension of Authorizations - (Sec. 2701) Terminates all authorizations contained in Titles XXI through XXVI of this Division on October 1, 2009, or the date of enactment of an Act authorizing funds for military construction for FY2010, whichever is later, with exceptions. (Sec. 2702) Extends certain prior-year military construction projects. Title XXVIII: Military Construction General Provisions - Subtitle A: Military Construction Program and Military Family Housing Changes - (Sec. 2801) Increases from $45 million to $50 million the maximum annual authorized obligation for emergency military construction. (Sec. 2802) Amends the MCAA for Fiscal Year 2004 to extend through FY2007 the temporary, limited DOD authority to use O&M funds for construction projects outside the United States during a declaration of war, national emergency, or contingency. (Sec. 2803) Repeals the requirement that military department Secretaries consult with the Secretary of Housing and Urban Development (HUD) on the availability of suitable alternate housing before entering into contracts to construct authorized family housing units in the United States. (Sec. 2804) Allows the Secretary of the Army to authorize family members of a member serving on active duty and assigned to a family-member-restricted area to remain in the leased housing unit until the military member completes the assignment. Terminates such authority at the end of FY2008. (Sec. 2805) Directs the Secretary to identify and consider alternative and more efficient uses for general and flag officer housing units that exceed 6,000 square feet. (Sec. 2806) Revises congressional notification requirements in connection with cost increases, cost decreases, or a reduction in the scope of work in connection with military construction projects. (Sec. 2807) Requires military department Secretaries to ensure that floor areas of unaccompanied housing does not exceed floor areas of similar housing in the local private sector. (Sec. 2808) Prohibits the Secretary concerned from carrying out a military project to construct a facility to provide training in urban operations for military personnel or personnel of DOD or other federal agencies until: (1) the Secretary of Defense approves a strategy for training for operations in urban terrain; and (2) the Under Secretary of Defense for Personnel and Readiness makes certain certifications to the appropriate congressional committees. (Sec. 2809) Authorizes the Secretary to carry out military construction projects in connection with the DOD industrial facility investment program. Requires: (1) 21 days' prior notification to the defense and appropriations committees before carrying out such a project; and (2) an annual report from the Secretary to Congress on actions taken and savings realized. (Sec. 2810) Repeals a provision placing special requirements for military construction contracts on Guam. (Sec. 2811) Authorizes military department Secretaries, until the end of FY2008, to exchange excess DOD real property in return for the construction of new facilities. Authorizes such Secretaries to exchange property in order to support agreements to limit encroachments upon military training, testing, and operations. Requires advance congressional notification of the latter authority. Requires annual reports on exchanges to include information concerning excess DOD real property used for such exchanges. (Sec. 2812) Extends through FY2009 the authority for pilot projects for the acquisition or construction of military unaccompanied housing. Reduces from 90 to 30 days the congressional notification period in connection with such projects. Subtitle B: Real Property and Facilities Administration - (Sec. 2821) Expresses the sense of Congress that the Secretary, when acquiring land for military purposes, should make every effort to do so by means of purchases from willing sellers, and should employ condemnation, eminent domain, or seizure procedures only as a last resort in cases of compelling national security requirements. Requires the Secretary, before using any of the latter procedures, to notify the defense and appropriations committees at least 14 days in advance. Provides an exception to the advance notification requirement when delay would be detrimental to national security or the protection of health, safety, or the environment. (Sec. 2822) Consolidates and makes technical amendments to DOD authority regarding the granting of easements for rights-of-way. (Sec. 2823) Authorizes military department Secretaries to grant restrictive easements in connection with the conveyance of real property, including restrictions for conservation purposes (with limitations). Requires consent from proposed easement recipients. (Sec. 2824) Increases from five to ten years the maximum lease term for non-housing structures and real property relating to structures in foreign countries needed for purposes other than military family housing. (Sec. 2825) Consolidates provisions relating to the transfer of DOD real property within DOD and to other federal agencies. (Sec. 2826) Amends the MCAA for Fiscal Year 2006 to direct the Secretary, as part of a study of roads leading into a military installation that were highly impacted by defense base closures or realignments or the Integrated Global Presence and Basing Strategy, to determine whether: (1) the existing surface transportation infrastructure is adequate to support the increased traffic; and (2) the defense access road program adequately considers the complete range of surface transportation options necessary to support the national defense. (Sec. 2827) Requires a report from the Secretary of the Army to the defense and appropriations committees analyzing the potential expansion of the Pinon Canyon Maneuver Site (Pinon Site) at Fort Carson, Colorado. Prohibits such Secretary from carrying out any acquisition of real property to expand the Pinon Site until 30 days after submitting the report. Requires such Secretary to report to such committees an assessment of the operational ranges used to support range activities. Subtitle C: Base Closure and Realignment - (Sec. 2831) Authorizes the Secretary to deposit into the Department of Defense Base Closure Account 2005 lease proceeds received as a result of 2005 base closure and realignment decisions. (Sec. 2832) Directs the Secretary of the Air Force to report to Congress on Air Force planning for future roles and missions for active and Air National Guard personnel and installations affected by decisions of the 2005 round of defense base closures and realignments. Subtitle D: Land Conveyances - (Sec. 2841) Authorizes the Secretary of the Army to convey to Jefferson County, Arkansas, an easement for the benefit of Pine Bluff Arsenal, Arkansas, if such Secretary determines that the conveyance and subsequent easement use will not adversely impact the mission of the Arsenal. Makes the sole purpose of such conveyance the construction, maintenance, and operation of a railroad. (Sec. 2842) Amends the NDAA for Fiscal Year 1997 to increase the total acreage relating to a land transfer at the Potomac Annex, District of Columbia. (Sec. 2843) Directs the Secretary of the Navy to convey to any public or private person or entity outside of DOD specified real property at the former Naval Air Station Barbers Point, Oahu, Hawaii, for the purpose of promoting its beneficial development. (Sec. 2844) Authorizes the Secretaries of the Army and Navy to convey to the Metropolitan Community College Area in Omaha, Nebraska, certain property under the control of the Army Reserve and Navy Reserve for educational purposes. (Sec. 2845) Authorizes the Secretary of the Army to convey to the town of Hopkinton, New Hampshire, the Kast Hill property in Hopkinton, in order for the town to use its existing sand and gravel resources and to ensure perpetual conservation of the property. (Sec. 2846) Authorizes the Secretary of the Army to convey to the North Allegheny School District specified real property at the North Hills Army Reserve Center in Allison Park, Pennsylvania, for educational and recreational purposes and related parking facilities. (Sec. 2847) Authorizes the Secretary of the Army to transfer to the Secretary of Veterans Affairs a portion of Fort Jackson, South Carolina, for use as a veterans' cemetery. (Sec. 2848) Expresses the sense of Congress that the Secretary of the Army should consider the feasibility of conveying the Army Reserve Center in Marshall, Texas, to the Marshall-Harrison County Veterans Association, for the erection of a veterans' memorial, park, and museum. (Sec. 2849) Amends the MCAA for Fiscal Year 2002 to: (1) increase the amount authorized for the construction of a security barrier at the Engineering Proving Ground in Fort Belvoir, Virginia; and (2) authorize the Secretary of the Army to enter into an alternate agreement for the construction of a road in connection with a military construction project there. (Sec. 2850) Authorizes the Secretary of the Army to convey to the Department of Veterans' Services of the Commonwealth of Virginia specified real property at the Radford Army Ammunition Plant, Virginia, in order to establish and operate a state-run veterans' cemetery. Subtitle E: Energy Security - (Sec. 2851) Consolidates into a new chapter under federal armed forces law provisions concerning energy efficiency and conservation within DOD facilities and activities. Directs the Secretary to: (1) submit annually to the defense and appropriations committees DOD energy performance goals regarding transportation systems, support systems, utilities, and infrastructure; and (2) develop and update a comprehensive plan to help achieve DOD energy performance goals. Requires reports concerning progress made in achieving such goals to be submitted to the defense and appropriations committees (currently, Congress). Repeals federal provisions concerning energy savings at military installations. (Sec. 2852) Establishes as a DOD goal to: (1) produce or procure not less than 25% of the total electric energy it consumes during FY2025 and thereafter from renewable energy sources; and (2) produce or procure such renewable energy when it is life-cycle cost-effective to do so. (Sec. 2853) Requires a 30-day prior notification to the appropriate congressional committees before the Secretary may award an energy savings performance contract that contains a clause setting forth a cancellation ceiling in excess of $7 million. (Sec. 2854) Directs the Secretary to ensure, to the maximum extent practicable, that energy efficient products meeting DOD requirements are used in new facility construction if such products are readily available and their use is consistent with DOD energy performance goals and the DOD energy performance plan. Subtitle F: Other Matters - (Sec. 2861) Authorizes the Secretary to award grants, conclude cooperative agreements, and enter into contracts to conduct research and technical assistance in connection with the Defense Economic Adjustment Program. (Sec. 2862) Authorizes the use of grants for addressing the encroachment of state-owned and operated National Guard facilities that are subject to significant training use by the Armed Forces. (Sec. 2863) Prohibits the Secretary of the Navy from entering into any agreement authorizing the use by civil aircraft of marine and naval air stations in Camp Pendleton, Miramar, and North Island, California. (Sec. 2864) Modifies authorized project purposes for a construction project at Rickenbacker Airport, Columbus, Ohio, and certain highway projects in Detroit, Michigan, under the Safe, Accountable, Flexible, Efficient Transportation Equity Act: A Legacy for Users. (Sec. 2865) Provides for the availability of funds for the South County Commuter Rail project in Providence, Rhode Island, under the above Act. (Sec. 2866) Requires the Secretary of the Army, within two years after the enactment of this Act, to assume responsibility for the annual O&M of the Fox Point Hurricane Barrier in Providence, Rhode Island. Authorizes appropriations. (Sec. 2867) States that the Federal Transit Administration's Dear Colleague letter dated April 29, 2005, which requires fixed guideway projects to achieve a "medium" cost-effectiveness rating in order to be recommended for funding, shall not apply to the Northstar Corridor Commuter Rail Project in Minnesota. (Sec. 2868) Directs the Secretary of the Army to report to Congress evaluating the costs, benefits, feasibility, and suitability of locating support functions for Fort Belvoir and the Engineering Proving Grounds, Virginia, on property currently occupied by GSA warehouses in Springfield, Virginia. Division C: Department of Energy National Security Authorizations and Other Authorizations - Title XXXI [sic] - Department of Energy National Security Programs - Subtitle A: National Security Programs Authorizations - (Sec. 3101) Authorizes appropriations to the Department of Energy (DOE) for FY2007 for: (1) activities of the National Nuclear Security Administration (NNSA) in carrying out programs necessary for national security, with specified allocations for weapons activities, defense nuclear nonproliferation activities, naval reactors, and the Office of the Administrator for Nuclear Security (Administrator); and (2) environmental restoration and waste management activities in carrying out national security programs, with specified allocations for defense environmental cleanup, other defense activities, and defense nuclear waste disposal. Subtitle B: Program Authorizations, Restrictions, and Limitations - (Sec. 3111) Amends the Atomic Energy Defense Act to direct the Secretary of Energy (Secretary, for purposes of this title only) to: (1) develop a plan containing specified objectives to transform the nuclear weapons complex so as to achieve a responsive infrastructure by 2030; and (2) report to the defense and appropriations committees on plan results. (Sec. 3112) Amends the NDAA for Fiscal Year 2004 to extend through FY2013 DOE's facilities and infrastructure recapitalization program. (Sec. 3113) Amends the Reagan Act to authorize the Secretary to enter into agreements for the utilization of contributions to the Global Threat Reduction Initiative. Requires an annual report from the Secretary to the defense and appropriations committees on the receipt and use of such contributions. (Sec. 3114) Authorizes the Secretary to enter into agreements for the utilization of contributions for the Second Line of Defense program. Requires an annual report from the Secretary to the defense and appropriations committees on the receipt and use of such contributions. (Sec. 3115) Amends the Atomic Energy Defense Act to extend through FY2008 the authority for appointment in DOE of certain scientific, engineering, and technical personnel. (Sec. 3116) Directs the: (1) Secretary to contract with the National Research Council of the National Academy of Sciences for a study of the quantification of margins and uncertainty methodology used by the national laboratories for assessing and certifying the safety and reliability of the nuclear stockpile; and (2) Council to report study results to the Secretary and the defense committees. Provides study funding. (Sec. 3117) Consolidates under DOE the counterintelligence programs of DOE and the NNSA. Requires the transfer of all functions, funds, and assets required by such consolidation by the end of FY2010. Amends the National Nuclear Security Administration Act to establish the position of NNSA Intelligence and Counterintelligence Liaison. (Sec. 3118) Amends the Atomic Energy Defense Act to require the Secretary to notify the defense and appropriations committees at least 30 days in advance of entering into a third party financing arrangement: (1) in connection with a project using DOE national security funds; and (2) involving a contractor or federal agency obtaining and charging to DOE as an allowable contract cost the use of office space, facilities, or other real property assets with a value of at least $5 million. Provides exceptions. (Sec. 3119) Amends the Departments of Commerce, Justice, and State, the Judiciary, and Related Agencies Appropriations Act, 1998 to extend through November 26, 2012, the deadline for completing certain land transfers to Los Alamos County, New Mexico, and of lands in trust for the Pueblo of San Ildefonso. (Sec. 3120) Limits to 90% of appropriated funds the availability of DOE defense environmental cleanup funds for the Waste Treatment and Immobilization Plant until the Secretary makes certain certifications to the defense and appropriations committees with respect to such Plant. (Sec. 3121) Requires a report from the Secretary to the defense and appropriations committees on the Russian Surplus Fissile Materials Disposition Program. (Sec. 3122) Prohibits the obligation of DOE defense nuclear nonproliferation funds for a construction project at the Mixed-Oxide Fuel Fabrication Facility until 30 days after the Secretary provides to the defense and appropriations committees an independent cost estimate and a certification with respect to Facility activities, as well as a corrective action plan for addressing certain Facility issues raised by the DOE Inspector General. (Sec. 3123) Directs the: (1) Secretary to study the feasibility and merit of establishing a targeted scholarship or fellowship program to educate future nuclear engineers at the postsecondary and postgraduate levels; and (2) President to report on such study to the defense and appropriations committees. Title XXXII: Defense Nuclear Facilities Safety Board - (Sec. 3201) Authorizes appropriations for FY2007 for the Defense Nuclear Facilities Safety Board. Title XXXIII: National Defense Stockpile - (Sec. 3301) Authorizes the National Defense Stockpile (NDS) Manager, during FY2007, to obligate up to $52,132,000 of the funds in the National Defense Stockpile Transaction Fund (Fund) for authorized Fund uses, including the disposition of hazardous materials that are environmentally sensitive. Authorizes the NDS Manager to obligate amounts in excess of such amount 45 days after notifying Congress that extraordinary or emergency conditions necessitate the additional obligations. (Sec. 3302) Amends the Thurmond Act and prior defense authorization Acts to authorize increased sales of NDS materials through specified periods. Title XXXIV: Naval Petroleum Reserves - (Sec. 3401) Authorizes appropriations to the Secretary of Energy for FY2007 to carry out activities relating to the naval petroleum reserves. Title XXXV: Maritime Administration - (Sec. 3501) Authorizes appropriations to the Secretary of Transportation (Secretary, for purposes of this title only) for FY2007 for the Maritime Administration for: (1) operation and training; (2) certain ship repair reimbursement under the Maritime Security Act of 2003; (3) assistance to small shipyards and maritime communities under the NDAA for Fiscal Year 2006; (4) the disposition of obsolete vessels in the National Defense Reserve Fleet; and (5) certain administrative expenses under the Merchant Marine Act, 1936 and the above Acts. (Sec. 3502) Prohibits the transfer of a Maritime Security Fleet operating agreement to a person not a citizen of the United States unless the Secretary of Defense determines that there is no U.S. citizen interested in obtaining the agreement. Requires that, in order for a vessel to be considered eligible for an operating agreement that is to be transferred, the vessel must meet specified DOD requirements for that operating agreement. Provides an alternative for operators of tankers under the Maritime Security Fleet program to meet U.S.-built replacement vessel requirements. Establishes a priority for the allocation of payments to vessels in the event that amounts available are insufficient to pay the full amount authorized under each agreement. (Sec. 3503) Amends the Merchant Ship Sales Act of 1946 to make applicable to Maritime Administration vessels activated in support of DOD missions limitations on the overhaul, repair, and maintenance of U.S. vessels in foreign shipyards. (Sec. 3504) Authorizes the Secretary to transfer or otherwise make available to any other department a vessel under the jurisdiction of the Department of Transportation, upon request of the Secretary of that department. (Sec. 3505) Amends the Merchant Marine Act, 1936 to exempt from certain commitment agreement requirements graduates of the U.S. Merchant Marine Academy who serve a five-year period of active duty in the Armed Forces, the National Oceanic and Atmospheric Administration (NOAA), or the Public Health Service. (Sec. 3506) Requires the Secretary of Defense, the Secretary of the department in which the Coast Guard is operating, the NOAA Administrator, and the Surgeon General of the Public Health Service to report on the status of obligated service of graduates of the Merchant Marine Academy, including those determined to have failed to comply with service obligation requirements. (Sec. 3507) Directs the Secretary of Transportation to transfer to the Secretary of the Navy during FY2007 no fewer than three combatant vessels in the nonretention fleet of the Maritime Administration. (Sec. 3508) Amends the Merchant Marine Act, 1936 to include service in the Coast Guard Reserve as qualifying duty for the receipt of student incentive payments. (Sec. 3509) Establishes crew requirements for U.S. large passenger vessels, including citizenship or lawfully admitted alien requirements for unlicensed seamen serving on such ships. Prohibits more than 25% of a crew from being lawfully admitted aliens or work-permitted aliens. Provides: (1) special rules for certain unlicensed seamen, including completion of a government security check or employer background check; and (2) work restrictions for such seamen. (Sec. 3510) Provides funding for an intermodal or marine facility comprising a component of the Hawaii Port Infrastructure Expansion Program.