I really liked the Trans America a lot and highly recommend it. If you want to branch off from it, I'd suggest detouring on a side trip to Glacier NP. If you have 11 weeks you should have time for that.
It's quite possible to start on the Northern Tier into Glacier National Park, take the Great Parks south to Missoula, and then hook up with your choice of Lewis and Clark or Trans Am. Glacier was stunning, and if they're still running the shuttle bus, you can see the Going to the Sun road without any effort. The passes in Washington are, erm, also memorable.
On the AC routes question, once you have a general route, the AC maps are perhaps most useful to locate services in the west. There's only one road from the Dubois to Rawlins, WY, for example; but knowing where there's a store, or a campground, or motel, isn't so easy. Further east, you don't usually have so many miles between services, but it's useful to have the route selected from a maze of twisty little roads, all different. That's why Fred's suggestion is so good (stay on an AC route for 1,000 miles) -- the midwest is a good place to start picking your own route.