I should have added, this issue was experienced when modifying the FBS/FCS mod files. I just retried with the Standard fileset and had no issue with any of my attempts to drop a conference below 12, increase a conference above 12, create a new conference, and create a new team. I think I'll work from that as a base, and work through the names and logos myself.
I gotta say, this is the first time I've found a game that looks like it can accommodate my weird desires to bend/realign/reorganize CFB from the ground up. I am in love with how open ended this seems, given my dive into these files. Thank you for your work on the project!
Second this - would be nice to be able to realign conferences, create teams, etc from in the game. From my general poking around (and ignore me entirely if I'm off base), this seems to only be done through XML right now. Certainly not a deal breaker, and I still need to get my feet wet in the UI but I'm enjoying it a lot so far.