I recently replaced the tranny in my 90 lumina 3.1L (auto). what could cause the battery to boil (other than the obvious crossing of wirers) while replacing the tranny, the car also sat for a month before I had the time to do the work... did I miss something while putting the damn thing back togeather??

No, the regulator on the alternator has probably failed.
Check the voltage at the battery, it is probably 17 or higher.

I agree with 300+, either your alternator is always charging, or you have a shorted wire to the regulator that is keeping it constantly engaged. It is possible that you pinched some wiring between the trans and the engine which could cause it to overcharge