Pull up resistors tie logic states high (a digital "1" or 5v), rather than leaving the logic state "floating" (ie. neither high or low). Many switches on these older machines or even some old game system controllers have pull-up resistors so that the logic state of the input to other circuitry is known/guaranteed. It just means the logic state of an input (be it transistor, IC, etc) is being forced to a "1" (5v) or a "0" (0v) and not left undecided.

Hope that helps

There's a lot of things that could be the issue, that's what makes diagnosing fun (or a *real* PITA depending on the day). Voltage feeding back into a circuit, bad capacitor somewhere in the circuit.. broken/cold solder joint on the board(s) or something with the wire harnesses. I had a machine where you'd hit the flipper button & it would go into self test mode. Turned out to be a bad capacitor on the MPU board (I think for the diagnostic switch circuit). Took me *forever* to figure out that one.

It looks like you've done quite a bit of work replacing components on the boards. A lot of people have different philosophies toward that and mine is generally if it ain't broke, don't fix it. Most of the old electronics in these machines are still working very well and will continue to work well for years and years -- exceptions would be some of the electrolytic capacitors used on any pinball machine that's 20-30 years old since they dry out over time. If there's burnt connectors, broken or melted parts, alkaline damaged parts, definitely replace those -- otherwise just replacing everything cause it's old will cost a lot of $$$ when it's really not necessary.

Anyway, with most issues the easiest way to diagnose is if you have a few spare boards around so you can knock the issue down to a particular board. Sometimes you don't have that luxury and have to look at the schematic and logic through things.. then investigate with a multimeter and logic probe. Sometimes this stuff defies logic =) I had 1n4004 diodes on the solenoid board of a Stern Nugent machine that were bad and causing the pop bumpers to work intermittently -- they tested fine with the diode test on the meter. It took me a while to decide to replace what amounts to a few cents in components just to see if it would work.. and it cleared up their random behavior.

If I were you I'd pull the MPU board & driver board and look for broken solder joints on the backside of each connector. Sometimes wiggling the connectors or tapping lightly on the board can expose issues with broken solder connections. Then.. go from there