I don't mean to necropost but I often think of this exercise, certainly a daunting proposition. The Corp of Discovery Expedition illustrates several of the challenges and hardships one would encounter.
It seemed that information that gives one foresight to possible routes would be very beneficial....
It occurs that rail road routes could be a good reference as they required certain parameters in order to be built, grade, routes, terrain, etc... It seemed there must be more specific information available that would be helpful to the journey... similar to a road atlas. Turns out there is information about routes and details. One such example is from the partnership of Kit Carson and John Fremont.
" The Exploring Expedition to the Rocky Mountains and Northern California"
Narrative:
http://www.biodiversitylibrary.org/item/96822#page/1/mode/1up
In it's day it was used as an atlas, a travel guide, and an adventure read.
Kit Carson story:
https://www.youtube.com/watch?v=XLxsSGO2VWE
21 minute mark...
Next trip across the country might have a few detours to explore some of the history.