Wow, bikepacking the CDT. That's a serious endeavor to consider, and quite a mapping / planning project, too. Cool.
The wilderness file is all federally designated wilderness, whether forest, blm, national park or monument. It does not show wilderness study areas or plain old national parks and monuments.
In other words, just because it's not in the yellow areas doesn't mean it's bike legal. But for the most part, it does.
TF can open GIS shapefiles, but I don't know of any good ones that show other useful boundaries. If you do find any, I'd be curious to see them and can help converting if necessary.
Also, carrying a bike is technically not legal in wilderness. I have checked and double checked (and I worked as a wilderness ranger once). National Park is often OK, but wilderness, no.
I'd love to talk more. Have you seen the bikepacking.net site?