Here is an alternate version, although at this point I am not sure what is more accurate. Big props to r/CFB which weighed in with some good knowledge and advice on the map. I did also use Common Census to influence my decisions where I was unsure, but did not rely too heavily on it. Most of the changes were in Upper Michigan, Dakotas and Montana, Florida, Texas, Georgia and NC.
The major change is the inclusion of some FCS teams. I used attendance data to include the most popular teams in FCS (since including them all would be insane and would clutter the map up). The FCS teams included are: Montana, Montana State, North Dakota State, Georgia Southern, Delaware, Jackson State, Jacksonville State, and Old Dominion. Also added were FCS schools set to join FBS in the coming years. That includes: UMass, Texas State, and UTSA.
Final thing is that I swapped in some better logos in some places. SDSU, UNLV and Utah State get their athletic logos in there instead of the school logo, and UWashington got their more traditional W logo, which I guess is preferred by the fan base. Also, Army didn't actually have their logo on the previous map (it was on a covered layer in the editable file). There might be some other logo swaps I forgot about.
I don't think I'll be making anymore edits to the map.
Edit: Added Temple, it seems like I had totally forgotten about them. My bad.