Echoing some of the thoughts on doing things more "creatively," as it were, a couple of points I'd like to make:
a. I don't think we should be making a huge deal of the number 32. Correct me if I'm wrong, but as I understand it, there's still a lot of time left for people to submit schools, and I've heard of at least a couple of people that are considering joining who aren't on the map yet, so I certainly don't think we should necessarily split teams into 4 conferences of 8 and act like it's set in stone.
b. In terms of conference games, I think it's fine to not have the same number of schools as long as each team still plays the same number of conference and non-conference games. Obviously, not everyone will have a perfect schedule within their conference every year if that's the case, but that's not the case in real life either, and I think it's something we can work with. (Personally, I'd prefer erring on the side of larger conferences so we can avoid teams having to play each other twice in the same year, but I'm open to whatever.)
c. I don't want to make things too difficult setting things up, but pinballing off of Dan's suggestion, would it be at all possible to let the legacy project dictate part of the conference layout? Given how much conference switching goes on in the real world, it seems to me like schools that would have been better over the course of history would gravitate towards the same, prestigious conferences. Maybe an easier way to do that would be to just run the legacy project with "dummy" conferences and then allow some teams to switch based on whatever history we come up with. Either way, just something to chew on.