I just got the game up and running again a few days ago. Before doing a big tear down to deep clean I'd like to try and resolve two issues.
1. Spinner star rollover does not register in game play but it registers fine in test mode. (Switch number 320)
2. The game does not advance to ball 2 after ball 1 drains. After what technically is ball 2 drains it then advances to ball 2 and from there on out advances balls correctly. Basically your getting an extra ball, regardless if its set to 3 or 5 ball game.
3. Think this isn't an issue but found what I believe is an erroneous diode on one of the switches of the right slingshot. The way it soldered on I don't believe its serving any purpose. The other two slingshots do not have a diode on the same switch. Diode in question is circled in one picture, the other switch picture is the other switch for the same slingshot.

It is an original non battery damaged MPU. Power supply rebuilt, every electrolytic cap replaced. Replaced the ceramic caps on MPU. Have a remote battery on MPU now and reset all audits after attaching that to MPU. No garbage on displays, besides those two issues currently everything else seems to be working fine. I have not replaced the header pins on MPU yet. I did find that on a couple dip switches there was no continuity across the dip switch when flipped to ON, rocked those switches a few times and then they worked. I tried all dips off and ball count error still occurs. Manual mentions in switch test that there will always be a switch closed called the Chuck-A-Luck switch?? Is that a mistype talking about another game. When I enter switch test with ball removed no switches are activated. I mapped the switches to a matrix chart but I don't fully understand how to interrupt it. On the chart switch 050 should be coin chute 1, my two coin chutes registered 060 and 070.

Thanks in advance for the help!

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Update: The extra ball was being given because I never set new score levels for extra ball after resetting all settings. Set score levels up and ball count is working.

But now my game over light is stuck on. Replaced the associated MCR106 but that did not fix it, if I ground the gate on the MCR the lamp does turn off. Resistors check out okay for that lamp on lamp board. I have spare decoder chips so may replace U3 and hopefully that fixes it, other wise it may be the buffer chip which I don't have any of on hand.

Still cannot figure out the switch that works only in test mode but not in game play.

Update: Spoke with Jim at Echo Lake Pinball and determined that the rollover switch may not be an issue. When you rollover that switch it is suppose to turn on the insert for the spinner "1000 Points when lit". I found out that the insert lamp is stuck off. Replaced the MCR106 associated with that lamp but no change. The lamp does turn on briefly at first power up and that is it. So I have my game over lamp stuck on and the spinner insert lamp stuck off. Both are MCR106, both have been replaced, resistors associated with both lamps check okay in circuit so still suspecting the 4050 buffer chip but don't have any on hand right now. I also already tried a new decoder chip U3 as both lamps run through that, but again no change in behavior.

Ended up being a faulty 4050 buffer chip. Replaced that and both game over light and spinner "1000 when lit" insert function as they should. The switch that I thought was faulty is indeed fine, it only turns on that spinner insert and when the lamp wasn't working I thought the switch was the issue. Now onto full playfield tear down for deep cleaning.