Alright, having opto issues and finally decided it's time to try troubleshooting this legitimately. I played some games trying to get it to fail and have noticed a trend of the game deciding it's a good time to "Launch a probe" in the right gun...which is rather unusual.
I'd done final frontier and was working on the second round of borg locks. Had 2 locked, started Rescue mission, hit a couple targets and then hit the ball into the neutral zone. It for some reason counted it as my third lock. Neutral zone lock wasn't lit, and it is working, I went back to verify. Playing the mode like normal, losing a ball, and then it kicks a ball to the right gun and tells me to launch a probe right in the middle of multi-ball.
I've also gotten the balls confused in non-multi ball modes but usually upon exit with fast ball drains. EX. Ferengi when at 3 balls and lose two simultaneously. Sometimes when hitting the neutral zone but not activating the target it seems to spit a ball out the left VUK but not after listening the ball make it all the way through the subway. I suspect my issue must be related to the left side subway sometimes not properly counting. Though it's hard to keep a mental model of where the balls are.
I tried some of the obvious things. Looking to get more advanced. I've wiggled connectors in switch test on all trough connectors, no rogue readings. Pounded around the flippers, VUKs, Neutral zone area and no rogue readings there either. Used a plastic tool to interrupt all subway optos, and trough optos, all seem fine. Ran both the left and right subway diverter tests and the worked as expected.
Any advice on what I should check next?