Seems like there has got to be some sort of switch problem, so I would continue looking in that area. Put the game in switch test and test every switch in the game to make sure they all work, are adjusted properly and they all trigger just one switch. Then I would lightly bump the playfield with my palm and see if you get any intermittent switch closures in the switch test. Try this with balls in the locks too. Then lift the playfield and look at the wiring on every switch in the game for loose wires. Finally the one catch-all for this game is the stupid 40 pin connector on the MPU card. No matter what is wrong with this game, you have to wonder if it could be caused by that hideous connector. The less times it is cycled the better, but I think you might reseat it, if it hasn't been disconnected in a number of years.
Good luck. This is a fun game and will be worth your restoration time!!