Good call by deadringer, fixing that makes the AI put all the players on teams that need to be filled before free agency even starts (meaning they leave SS/R leagues open instead of Single-A). I think this should fix problems as by the time those leagues start, the draft will have occurred.
I think unfortunately that for the time being, I'm going to fix the problem with the Yankees past, fix the messed up affiliates, add major league coaches, tweak some ML ratings, and get this out the door as a firm release for now unless any other problems come up. I tried to get going on Single-A ratings but it is going to be such a huge task that I don't think I can do it all without going insane.
As a follow up to that, since I am more familiar with a lot of you, I'll be launching an online league here in the next few weeks using these rosters (hence the reason why my roster building time will be more limited). If anyone would be interested in a team, please let me know.