Amends federal transportation law to make certain Amtrak reforms and operational improvements, including: (1) state funding of Amtrak rail routes; (2) establishment of improved financial accounting system; (3) development of a five-year financial plan; (4) improvement of passenger train performance; (5) establishment of an alternative passenger rail service program; (6) employee transition assistance; and (7) development of a Northeast Corridor state-of-good-repair plan.

Authorizes the Secretary of Transportation to make grants to an applicant state, Interstate Compact, or public agency to assist in financing the capital costs of facilities and equipment necessary to provide intercity passenger rail transportation.

Establishes: (1) a Next Generation Corridor Equipment Pool Committee; and (2) a rail cooperative research program.

Authorizes the Secretary of Homeland Security to make grants to Amtrak for certain systemwide security upgrades.

Authorizes the Secretary of Transportation to make grants to Amtrak for fire and life-safety improvements and infrastructure upgrades to tunnels on the Northeast Corridor.

Directs Amtrak to submit to the National Transportation Safety Board a plan to address the needs of families of passengers involved in rail passenger accidents.

Requires the Secretary of Transportation to report to Congress an assessment of the current system for preclearance and screening of rail and airline passengers and baggage, as well as freight railroad traffic, between the United States and Canada.

Allows a tax credit to holders of rail infrastructure (intercity rail facility) bonds issued by a state, interstate compact, or Amtrak to finance or refinance certain rail improvement projects.

Authorizes the Secretary of Transportation (Secretary) to withhold up to one-half of 1% of certain funds for the costs of project management oversight of capital projects carried out by Amtrak.

(Sec. 103) Authorizes appropriations for costs associated with Amtrak early buyouts.

(Sec. 104) Authorizes appropriations for the portion of Amtrak's Railroad Retirement Tier II Tax which exceeds the Tier II annuities paid to Amtrak retirees.

Title II: Amtrak Reform and Operational Improvements - Amends federal transportation law to make certain Amtrak reforms and operational improvements.

(Sec. 201) Defines the national rail passenger transportation system as: (1) Amtrak's Boston-Washington Northeast Corridor; (2) high-speed corridors designated by the Secretary once they have been improved for high-speed service; (3) long-distance routes (of greater than 750 miles) operated on the date of enactment of this Act; and (4) short-distance routes operated by Amtrak or a non-Amtrak recipient of federal capital assistance.

Authorizes Amtrak and a state to agree on the operation of an intercity route or service not included in the national rail transportation system.

Declares that this Act does not preclude Amtrak from restoring, improving, or developing non-high-speed intercity passenger rail service.

(Sec. 202) Replaces the Amtrak Reform Board with a reconstituted Board of Directors of Amtrak, with revised composition requirements.

(Sec. 203) Authorizes the Amtrak Board of Directors to employ an independent financial consultant with experience in railroad accounting to assist Amtrak in improving Amtrak's financial accounting and reporting system and practices.

Requires the Amtrak Board to: (1) implement a modern financial accounting and reporting system that will produce accurate and timely financial information; and (2) develop a five-year financial plan.

(Sec. 205) Directs the Secretary to establish substantive and procedural requirements for grant requests, including a 30-day approval process.

(Sec. 206) Directs the Amtrak Board to develop and implement methodologies for allocating train route operating and capital costs among states and Amtrak.

(Sec. 207) Directs the FRA to obtain the services of an independent auditor or consultant to develop and recommend objective methodologies for intercity passenger routes and services. Authorizes appropriations.

(Sec. 208) Requires the FRA Administrator and Amtrak jointly to develop new or improve existing metrics and minimum standards for measuring the performance and service quality of intercity train operations.

(Sec. 209) Requires the Surface Transportation Board to: (1) investigate the causes of any passenger train performance of under 80% for any two consecutive calendar quarters; (2) determine if delays or failure to achieve minimum standards can be attributed to a rail carrier's failure to prefer Amtrak over freight transportation; and (3) assess appropriate penalties upon a host rail carrier for such delays or failures.

(Sec. 210) Requires Amtrak to evaluate the performance of long distance passenger rail routes, and develop a performance improvement plan for them.

(Sec. 211) Directs the FRA to establish an alternative passenger rail service program.

(Sec. 212) Directs the Secretary to develop an employee transition assistance program for Amtrak employees adversely affected by the cessation of a long distance or any other route previously operated by Amtrak. Authorizes appropriations.

(Sec. 213) Requires Amtrak to develop a Northeast Corridor state-of-good-repair plan.

(Sec. 214) Directs the Secretary to establish a Northeast Corridor Infrastructure and Operations Advisory Commission and a Northeast Corridor Safety and Security Committee.

(Sec. 215) Authorizes the Secretary of the Treasury to make agreements to restructure Amtrak's long-term debt and capital leases.

(Sec. 216) Directs Amtrak to evaluate improvements necessary to make all existing stations readily accessible to and usable by individuals with disabilities.

(Sec. 217) Encourages the Amtrak Board to develop an incentive pay program for Amtrak employees.

(Sec. 218) Provides for state access to Amtrak equipment and services.

(Sec. 219) Repeals Amtrak self-sufficiency requirements.

(Sec. 220) Encourages Amtrak to increase its operation of trains funded by the private sector to minimize the need for federal subsidies.

(Sec. 221) Requires Amtrak to develop and implement a plan to improve on-board service.

Title III: Intercity Passenger Rail Policy - (Sec. 301) Authorizes the Secretary to make grants, meeting specified requirements, to an applicant state, group of states, Interstate Compact, or public agency to assist in financing the capital costs of facilities and equipment necessary to provide intercity passenger rail transportation.

(Sec. 302) Authorizes states to prepare and maintain a state rail plan that: (1) sets forth state policy involving freight and passenger rail transportation (including commuter rail operations); and (2) includes a long-range rail investment program. Requires the Secretary to prescribe procedures for the review of state rail plans.

(Sec. 303) Directs Amtrak to establish a Next Generation Corridor Equipment Pool Committee to design, develop specifications for, and procure standardized next-generation corridor equipment.

(Sec. 304) Sets forth additional duties of the FRA Administrator, including to provide assistance to states in developing state rail plans, and to develop a long-range national rail plan. Requires the Administrator to develop a schedule for achieving specific, measurable performance goals.

(Sec. 305) Directs the Secretary to establish a rail cooperative research program to address intercity rail passenger and freight rail services, including ways to expand the transportation of international trade traffic, enhance the efficiency of intermodal interchange at ports and other intermodal terminals, and increase availability of rail service for seasonal freight needs. Directs the Secretary also to establish an advisory board to recommend research, technology, and technology transfer activities related to rail passenger and freight transportation.

Title IV: Passenger Rail Security and Safety - (Sec. 401) Authorizes the Secretary of Homeland Security to make grants to Amtrak for certain systemwide security upgrades. Authorizes appropriations for FY2006-FY2008.

(Sec. 402) Authorizes the Secretary to make grants to Amtrak for fire and life-safety improvements and infrastructure upgrades to Amtrak tunnels on the Northeast Corridor. Authorizes appropriations for FY2006-FY2008.

(Sec. 403) Directs Amtrak to submit to the National Transportation Safety Board (NTSB) a plan to address the needs of families of passengers involved in rail passenger accidents. Authorizes appropriations for FY2006.

(Sec. 404) Requires the Secretary to report to Congress an assessment of the current system for preclearance and screening of rail and airline passengers and baggage, as well as freight railroad traffic, between the United States and Canada.

(Sec. 405) Directs the Secretary of Homeland Security, in cooperation with the Secretary through the Assistant Secretary of Homeland Security (Transportation Security Administration (TSA)) to study and report to Congress on the feasibility of requiring security screening for passengers, baggage, and cargo on passenger trains, including an analysis of any passenger train screening pilot programs undertaken by the Department of Homeland Security. Authorizes appropriations for FY2006.

Title V: Rail Bond Authority - (Sec. 501) Authorizes the Secretary to designate rail infrastructure bonds, to be issued by a state, a group of states, or by Amtrak, and which shall be known as Section 54A bonds for purposes of Section 54A of the Internal Revenue Code (relating to credit to holders of qualified rail infrastructure bonds). (Section 54A has yet to be enacted.)