Here is a place with the route on GPS for download, might take some conversion software... not sure how detailed.

http://www.travelbygps.com/guides/lewis_clark/lewis_clark.php

Also a trail on Google Earth, maybe copy and edit to create road route.

http://www.gearthblog.com/blog/archives/2005/11/lewis_and_clark.html

And another..

http://googlemapsmania.blogspot.com/2009/03/lewis-clark-trail-on-google-maps.html

Page with "View Map" button takes you into a Google map, section by section as selected. You can easily see the local county/state highways that follow the trail most closely. It has various waypoints, but not bars/diners, but more parks, museums, etc... but it does have motels/inns/b&bs (useful).

http://lewis-clark-trail.us/

If you can export to your own Google map, you can search stretches for destinations (road house, etc...), save your own MyMap. You got me thinking, I just might start creating this...

CHUCK