I have sad update to this story. It seems the incorrect driver board was installed in this machine prior to me buying it. T2 is a pre-fliptronics game, and should be using a A-12697-1 board. It does have a A-12697-3 board in it which doesn't have the opto's two big resistors, and a flipper relay. (and probably other stuff)
(This was a Wolfman machine). So, anybody got any suggestions short of buying a whole new driver board? is it possible to add the pre-fliptronics components to make it a -1? Anyone ever come across anything like this? I already put a lot of replacement parts in, big caps, bridge rectifiers, chased my tail to provide 5v to the watchdog chip so it would stop resetting when both flippers were hit at the same time! The photo shows some of the missing components.