Thru-hiker, Jonathan Ley makes a CD that has all the maps of the CDT. You print them out on your home computer. They have been updated for 2004 and now include a way to use a GPS with them. The route is marked on the maps along with alternate routes. He also includes notes.
To get BLM state maps call these numbers.
Montana http://www.mt.blm.gov/faq/maps/ Phone: (406) 896-5000
Idaho http://www.id.blm.gov/Phone: 208-373-4000
Wyoming http://www.wy.blm.gov/ Phone: 307-775-6256
Colorado http://www.co.blm.gov/mapinfo/mapfaq.htm Phone:(303) 239-3600
New Mexico http://www.nm.blm.gov/ Phone:(505) 438-7400