Lewis and Clark National Historic Trail Extension Act of 2003 - Extends the Lewis and Clark National Historic Trail to include: (1) the route followed by Meriwether Lewis and William Clark in the preparation phase of the expedition, starting at Monticello, located near Charlottesville, Virginia, and traveling to Wood River, Illinois, and in the return phase from Saint Louis, Missouri, to Washington, D.C.; and (2) designated Lewis and Clark sites in Virginia, D.C., Maryland, Delaware, Pennsylvania, West Virginia, Ohio, Kentucky, Tennessee, Indiana, and Illinois. Directs the Secretary of the Interior to complete a general management plan to include the extended route within three years from the date funds are first made available for that purpose.