I do a decent amount of day hiking in GNP and some backpacking. The map I have found useful is the National Geographic/Trails Illustrated Glacier Waterton Lakes National Parks map. It clearly shows the CDT route highlighted in yellow. It also shows topographic features, campsites, etc. I have been carrying it for about four years and it is now showing a few pinholes at the crossover folds—it is durable enough.
For the Bob Marshall area I carry the Bob Marshall Great Bear and Scapegoat Wilderness Areas USFS map 2011 version. This map is made from a similar durable "plasticized" paper and shows the CDT route on a topographic background.
There is a Falcon Guide book Hiking Montana's Bob Marshall Wilderness by Erik Molvar but it is not CDT-specific and is arduous to use as you must piece together many small segments to create a desired route. I just spent some time trying to trace the CDT through Molvar's book and it is tiresome and I am not certain that he covers all the CDT segments. There is probably something more appropriate.
For mileages and elevation change I like Hillmap.com and use it frequently.
I hope somebody can suggest some better guide books!
JK