The only issue is that, from my understanding, when teams are in an affiliated minor league but are not affiliated with any major league teams, they don't make any transactions or changes. They don't sign players or trade players or anything else. So you will have to maintain them, adding players to replace those who retire and so on.
I am interested in a very similar sort of fictional-but-realistic form of historical simming. When I get the chance, I plan on testing out a potential way of adding leagues, which I've described here:
http://www.ootpdevelopments.com/boar...d.php?t=132921
I have no idea if it will work the way I want it to. Feel free to try it yourself and let me know what the results are. I don't get much time to play the game, so I don't know when I'll be able to check this out.