This was literally a nightmare today. I figured I'd post my process so some of you can get a laugh, and maybe save someone a little time. This whole process took me hours. I should start out by saying I am not very familiar with this system. This is by no means the correct way to troubleshoot, just what I did to resolve it.

Problem: Flipper buttons don't work in menu. Shows constant pressing of both buttons in switch test.
Attempt 1: Game had some hacks and weird wiring. Check wiring, looks fine. Unplug all connections to buttons. Problem persists. Weird... Do a little research.

Attempt 2: Flipper board! I forgot they have a little flipper board under the playfield. It was unplugged. Plugged it in, right flipper is cured, left flipper constantly pressed. Do some more research....

Attempt 3: Test board. I'm not great with schematics, but this is a really simple board. I'm seeing 64v for the right flipper, that goes away when I hit the button. 26v for the left flipper, goes away when I press the button. Maybe the board is expecting 64v and thinks the button is pressed? I'm fairly certain I tried swapping this board when I had another System 3 here and it didn't help. I think the board is fine. Do some research....

Attempt 4: Fumble through schematics. Try to find the source of the 26v and why it isn't 64v. There is a fuse board under the playfield with a common line. Lets try and follow that back to the source! Schematic shows A9P3/J3 and in dotted lines shows relay panel. Spend a lot of time looking for a relay panel. There is no A9 board. Getting very frustrated. Eventually find A9P3, it's just a plug for disconnecting the playfield. It's a tiny bit loose, couldn't be... Nope. Take a break.

Attempt 5: Something has to be pulling down the voltage, maybe a bad coil? What if I disconnect every fuse, then I should be able to put them in one by one and isolate the problem. Disconnect all fuses, now it's zero volts. WTF??!! There are some old style relays in the cab that shut off power, this must be the relay panel. Manually press relay, no fuses attached- 64v! Install one fuse at a time until it drops. Right kicking target is the culprit. Didn't know that thing was supposed to kick. Ha! This has been a challenging game to revive. I don't know the game or the system and it was in rough shape. Test flipper buttons in menu... It works! Hopefully a bad diode or bad coil.

Attempt 6: Troubleshoot coil. Difficult spot to work on, pull the entire assembly. Coil tests 12 ohms, matches other like coils. Not bound up, everything looks fine. Cut diode, diode tests fine. Maybe the diode test isn't reliable. Install new diode, re-assemble. Put in fuse... voltage drops to 26v. Initial solder job looked factory. Could it be backwards? Check schematic, wiring is correct. Check wire color power from other coils on the fuse strip. Everything looks correct.
Maddening!

Attempt 7: Replace coil. Maybe my meter isn't telling the whole story, or something is intermittently shorting. I bet a Williams sling coil has to be similar resistance. I found one that measure 11.2. Close enough. Wait, I have the actual Gottlieb coil, very odd as I don't work on these often. Sometimes being a hoarder pays off. Install in game.... voltage drops. Damn it! Attach only power lug. Voltage stays. Problem has to be on the driver board.

Attempt 8: Troubleshoot driver board. Previous repair in this section. Black mark behind the board in the cabinet. Something went terribly wrong at some point. Test transistor, nope, its one of those mosfets. I never remember how to test these. Mosfet in question tests differently than the others, that's enough for me. Remove component. Previous repair lifted 2 traces. There is also a chip socketed upstream and a resistor that was replaced. I really hope I don't have to replace any of that. I was able to bend the legs of the chip to reach the next point in both cases eliminating the need for jumpers. I should have still stitched the through hole, I was missing continuity on the top of the board. There was no solder on the top of the board because of the missing eyelet. Solder on the top, everything has continuity. New Mosfet tests like the others. Fingers crossed.

Attempt 8.5: Feed the children, and myself.

Attempt 9: Replace and test board. Everything seems to work. Hopefully whatever caused the failure has been fixed and won't come back. I'm going to call it a success.

That is my long winded repair of a flipper button not working in the menu. I spent a lot of unnecessary time around attempt 4 fumbling through the schematics and reading online. I should have just used more mechanical common sense. In the end, I learned a bit about the System 3, and found a few problems with the game I didn't know existed. I found a mis-adjusted rollover, a non working pop bumper, and of course the kicker.