Never heard of the pinstadium lights connecting to the boards. They have power and then the wires/alligator clips to trigger from the GI/flashers from what I have seen. If you disconnect those all the way, does the game do anything at all?
If you had a connector from the pinstadium GI or flasher pins connected to your CPU board, you may have sent 6.3 or 12 volts to the board...