Emergency Supplemental Appropriations Act for Defense and for the Reconstruction of Iraq and Afghanistan, 2004 - Makes emergency supplemental appropriations for FY 2004 for military and foreign affairs operations concerning Iraq and Afghanistan, including for Iraqi relief and reconstruction. Title I: National Security - Chapter 1: Department of Defense-Military - Makes appropriations to the Department of Defense (DOD) for: (1) military personnel; (2) operation and maintenance (O&M); (3) overseas humanitarian, disaster, and civic aid; (4) the Iraq Freedom Fund; (5) procurement; (6) research, development, test and evaluation; (7) Defense Working Capital Funds and the National Defense Sealift Fund; (8) the Defense Health Program; (9) drug interdiction and counter-drug activities related to Afghanistan; and (10) the Intelligence Community Management Account. (Sec. 1104) Continues during FY 2004 the increased monthly rates of pay, currently authorized for FY 2003, for imminent danger special pay and the family separation allowance. (Sec. 1106) Allows DOD O&M funds to be used to: (1) provide logistical support to coalition forces supporting military and stability operations in Iraq; and (2) enhance the capability of the New Iraqi Army and the Afghan National Army to combat terrorism and support U.S. military operations in Iraq and Afghanistan. (Sec. 1109) Appropriates funds to DOD to be used only for recovery and repair of damage due to natural disasters, including Hurricane Isabel. (Sec. 1110) Earmarks specified O&M funds for the Commander's Emergency Response Program (urgent Iraqi humanitarian and reconstruction relief and assistance for the people of Afghanistan). Requires quarterly reports from the Secretary of Defense to the congressional defense committees regarding the use of such funds. (Sec. 1111) Requires a report from the Secretary to the defense committees describing an Analysis of Alternatives for replacing the capabilities of the existing Air Force fleet of KC-135 tanker aircraft. (Sec. 1112) Makes permanent (currently, applies only during FY 2004) the exemption from the requirement of payment of subsistence charges while hospitalized in a military facility for an enlisted member, former enlisted member, officer, or former officer who is hospitalized in a military facility because of an injury incurred: (1) as a direct result of armed conflict; (2) while engaged in hazardous service; (3) in the performance of duty under conditions simulating war; or (4) through an instrumentality of war. Amends the Department of Defense Appropriations Act, 2004 to make such exemption retroactive with respect to any period of hospitalization on or after September 11, 2001. Directs the Secretary of the military department concerned to refund any amount paid, or waive recovery of unpaid amounts, for such charges since that date. (Sec. 1114) Allows the administering Secretaries to provide to members of the Ready Reserve called to active duty any medical and dental screening and care necessary to meet applicable standards for deployment. Requires the Secretary concerned to notify such members of their eligibility for such screening and care. Terminates such authority on September 30, 2004. (Sec. 1115) Makes each member of the Selected Reserve and Individual Ready Reserve who is placed in a mobilization category (subject to being ordered to active duty involuntarily) eligible to enroll in TRICARE for self or family coverage and to receive benefits for any period that such member: (1) is an eligible unemployment compensation recipient; or (2) is not eligible for health-care benefits under an employer-sponsored health benefits plan. Directs the Secretary to: (1) provide for at least one open enrollment period each year; and (2) charge appropriate premiums for such coverage. Prohibits a member from enrolling in the TRICARE program while entitled to DOD transitional health care. (Sec. 1116) Sets forth conditions under which a member of the reserves who is issued a delayed-effective-date active duty order shall be treated as being on active duty for more than 30 days and therefore eligible for medical and dental care for active-duty personnel. Terminates such authority at the end of FY 2004. (Sec. 1117) Increases the benefit period for transitional health care authorized for members separated from active military duty from 60 to 180 days after separation. (Sec. 1118) Requires each member of the reserves who is called or ordered to active duty under a mobilization to be notified in writing of the expected duration of such mobilization. (Sec. 1120) Requires semiannual reports from the Secretary to Congress on the military operations of the armed forces and the reconstruction activities of DOD in Iraq and Afghanistan. (Sec. 1121) Appropriates funds to DOD for securing and destroying conventional munitions in Iraq, including bombs, bomb materials, small arms, rocket-propelled grenades, and shoulder-launched missiles. Chapter 2: Department of Homeland Security - Makes appropriations for the Department of Homeland Security for: (1) the Coast Guard for costs related to Hurricane Isabel damage; and (2) disaster relief. (Sec. 1201) Amends the Department of Homeland Security Appropriations Act, 2004 to make biodefense countermeasures funding subject to the authorization of the Project Bioshield Act of 2003. Chapter 3: Military Construction - Makes appropriations for military construction and military family housing O&M. (Sec. 1301) Authorizes the Secretary to use O&M funds for military construction projects in support of Operation Iraqi Freedom or the Global War on Terrorism. Limits the total cost of such projects to $150 million in FY 2004. Directs the Secretary to notify the defense committees within 15 days after any such obligation of funds. Requires quarterly reports from the Secretary to the defense committees on the worldwide obligation and expenditure of such funds. Title II: Iraq and Afghanistan Reconstruction and International Assistance - Chapter 1: Department of Justice - Makes appropriations for: (1) the Department of Justice for general legal activities; (2) diplomatic and consular programs and emergencies in the diplomatic consular service; (3) embassy security, construction, and maintenance; (4) contributions for international peacekeeping activities; and (5) international broadcasting operations. Chapter 2: Bilateral Economic Assistance -Makes appropriations for: (1) the United States Agency for International Development, including for the Capital Investment Fund; (2) the Iraq Relief and Reconstruction Fund for security, relief, rehabilitation, and reconstruction in Iraq; (3) the Coalition Provisional Authority in Iraq; (4) the Economic Support Fund; (5) international disaster and famine assistance; (6) international narcotics control and law enforcement; (7) nonproliferation, anti-terrorism, demining, and related programs; (8) the Foreign Military Financing Program; and (9) peacekeeping operations to support the global war on terrorism. (Sec. 2201) Prohibits the use of funds from this Act or the Emergency Wartime Supplemental Appropriations Act, 2003 (Emergency Wartime Act) to repay principal or interest on any loan or guarantee agreement entered into by the Government of Iraq with any private or public sector entity prior to May 1, 2003. (Sec. 2202) Prohibits funds made available from the Iraq Relief and Reconstruction Fund under either this or the Emergency Wartime Act from being used to enter into any Federal contract using other than full and open competition. Allows an exception only upon the written approval of the CPA Administrator and the head of the executive agency awarding and managing such contract. Requires, in any exception, the CPA Administrator or agency head to: (1) notify specified congressional committees at least seven days before such award; and (2) include a justification for the use of other procedures and related information. Prohibits the delegation of such notification. Makes this section: (1) inapplicable to contracts of less than $5 million and contracts authorized by the Small Business Act; and (2) applicable to the amendment, extension, or modification of prior contracts entered into using other than full and open competition. (Sec. 2203) Requires the CPA Administrator or head of any agency entering into a contract for assistance for Iraq using amounts from the Iraq Relief and Reconstruction Fund and using other than competitive procedures to publish and make public certain information with respect to such contract, including justification and approval documents. Makes this section inapplicable to contracts of less than $5 million and contracts authorized by the Small Business Act. (Sec. 2204) Amends the Emergency Wartime Act to extend through FY 2005 the authority of the President to: (1) suspend application of any provision of the Iraq Sanctions Act of 1990; and (2) export to Iraq, under certain circumstances, lethal military equipment designated by the Secretary of State for use by a reconstituted (or interim) Iraqi military or police force and small arms designated by such Secretary for use for private security. (Sec. 2206) Amends the Afghanistan Freedom Support Act of 2002 to increase from $300 million to $450 million the aggregate value of authorized assistance to the Government of Afghanistan and eligible foreign countries and international organizations to direct the drawdown of defense articles and services and military education and training. (Sec. 2207) Requires the Director of the Office of Management and Budget to submit to the appropriations committees, prior to the obligation of any funds from the Iraq Relief and Reconstruction Fund, reports on the proposed uses of all such funds for which obligation is anticipated during the three month periods beginning on January 5, 2004. Terminates such requirement on October 1, 2007. (Sec. 2211) Allows the Overseas Private Investment Corporation to undertake in Iraq any program authorized in title IV of the Foreign Assistance Act of 1961. (Sec. 2213) Extends through FY 2004 an exemption with respect to Pakistan on the prohibition of direct assistance to a country whose duly elected head of government was deposed by decree or military coup. (Sec. 2214) Amends the Afghanistan Freedom Support Act of 2002 to increase the authorization of appropriations for FY 2004. (Sec. 2215) Requires the CPA Administrator to report monthly until September 30, 2006, to the appropriations committees on Iraqi oil production, revenues, and uses of such revenues. Directs the Secretary of State to report to such committees on: (1) the debt incurred by the government of Saddam Hussein in Iraq and related matters; (2) U.S. efforts to increase resources contributed by foreign countries and international organizations to the reconstruction, rehabilitation, and peacekeeping efforts in Iraq; (3) addressing the needs of people with disabilities in programs, projects, and activities funded by the U.S. Government in Iraq and Afghanistan; (4) progress toward indicting and trying leaders of the former Iraqi regime for war crimes, genocide, and crimes against humanity; and (5) efforts of Iraqi officials and legal advisors to ensure that a new Iraqi constitution preserves religious freedom. Amends the Afghanistan Freedom Support Act of 2002 to require the Secretary of State to submit to specified committees reports on progress made in accomplishing the "Purposes of Assistance" set forth under such Act with respect to assistance provided for Afghanistan. (Sec. 2216) Prohibits funds under this Act from being obligated or expended in contravention of Articles 1 and 4 of the Optional Protocol to the Convention on the Rights of the Child on the Involvement of Children in Armed Conflict. (Sec. 2217) Requires activities carried out by the United States with respect to: (1) the civilian governance of Afghanistan and Iraq to include advice from women's organizations, to promote the high-level participation of women in future legislative bodies and ministries, and to ensure that human rights for women are upheld; (2) post-conflict stability in those countries to ensure that U.S. organizations that receive funding under this Act provide significant financial resources and assistance to counterpart organizations in such countries, to increase access of women to and ownership by women of productive assets, to provide long-term financial assistance for the education of girls and women, and to integrate education and training programs for former combatants; and (3) training for military and police forces in those countries to include training on the protection, rights, and particular needs of women. Title III: Inspector General of the Coalition Provisional Authority - (Sec. 3001) Establishes the Office of the Inspector General of the CPA. Requires quarterly reports from the Inspector General to the head of the CPA and to the appropriations, defense, and foreign relations committees summarizing activities of the Inspector General and the CPA with respect to obligations, expenditures, and revenues associated with reconstruction and rehabilitation activities in Iraq. Requires all such reports to be made available to the public. Authorizes the President to waive any report requirement for national security reasons. Terminates the Office six months after expiration of the authorities and duties of the CPA. Title IV: General Provisions, This Act - (Sec. 4002) Designates each amount provided in this Act as an emergency requirement pursuant to emergency legislation provisions of the congressional budget resolution for FY 2004 (H.Con.Res. 95). (Sec. 4003) Continues the eligibility of local educational agencies serving the children of military personnel to receive educational assistance payments under the Elementary and Secondary Education Act for children enrolled in such schools who lose their enrollment eligibility status due to the military deployment of both parents or legal guardians or of a parent or legal guardian having sole custody, or due to the death of a military parent or legal guardian while on active duty, as long as the child or children continue to attend the same local educational agency.