We have not followed much of their trail but did stop at the great musuem in Nebraska City, the historical site along the Natchez Trace and saw the statue in St. Louis beside the river.
Much of thier "trail" was on the rivers as much as possible and unless you want to get the rig pretty wet sticking to the "high points" is the best! sorry just had to throw that in.
I'm not sure where you can find a map of thier trail and find roads that will take you to all the historical sites, which is about all you can do in these modern times. I'll do a little research and add back what I can find.
I'm back...if you go to bing.com and type in Lewis and Clark Trail you will find many images that you should be able to print out then with an atlas find corresponding roads. As suggested the Natl. Park service may have a list of all the historical sites available.