I have attempted to map the train routes taken by Twain on this tour. 
This linked to page has six associated pages with route maps.  The 
routes are derived from kmz files from the University of Nebraska, 
reportedly for 1870.  Many are guesses of his routes as there are 
frequently alternative lines he could have taken and there is little or 
no discussion on the subject.

http://twainsgeography.com/content/our-fellow-savages-1869-70

The itinerary is from http://www.twainquotes.com/SpeechIndex.html for 
the most part and from the Day By Day site.