Couple things to consider on a sample TZ ...
1) all the wiring is STILL IN THE GAME for the removed optos ... in fact, you can purchase extra optos and wire them right back up, and the software will happily work with them ... in fact, if you put 9.4H in, you can reinstall the 3rd magnet and its optos, and the game'll do some neat multiball start tricks.
2) see 1) ... if one of those wires is pinched somewhere, you'll get false triggers on the unused switches
3) a sample TZ has TWO 7-opto PCBs ... just swap 'em, and see if the problem moves somewhere else.