The problems you are encountering in switch test are indicating you have shorted capacitors or diodes under the playfield on those specific switches, possibly more than one. Clip all the caps and test all the diodes associated with the switch numbers displaying multiple closures, then retest.

You may have given up to easily. Was there a cap on the outhole switch or the two tilt switches? I would remove those and retest.

The caps are a notorious problem and when I get a new Bally game now, my first step is to just remove them all. Then, I install new ones where needed (the only place I find they actually help are standup targets). Curse Bally for even using them at all!

Well, as others suggested, you are going to have to unplug the switch harnesses, then go in to switch test and connect a wire+alligator clips to check each input pin, unsung the schematics as you go to determine if the MPU is still displaying the wrong switch numbers in switch test with each wire. Or, just switch out the PIA as a shotgun approach. It really sounds like an MPU issue at this point.

However, if your wire+alligator clip test produces the correct results in switch test, you can start tearing apart the play field some more...