Sounds like you're having logic communication glitches. Carefully reseat the 6800 cpu, the two 6821s, the ROMs and the 5101 (USE STATIC CAUTION!). Basically all the MPU socketed chips. Be careful not to bend any legs under.

If all the other board connectors haven't been rebuilt they are probably in need of service like your rectifier connectors were.

Indeed, rebuild all of the connectors. Save yourself a lot of grief chasing gremlins.
Been there, done that on my Embryon & Mr & Mrs Pac man.

I would try a new 5101, it can cause strange things to happen.

I'm putting my money on 5101 being bad.

But the whole -35 needs updating if you want bulletproof gameplay:

https://pinside.com/pinball/forum/topic/vids-guide-quick-bally-driver-board-repair-bulletproofing

Could definitely be flaky logic or connectors, but I would put it into switch test and see if there's anything weird happening before diving into the MPU. Something funky in the switch matrix can also cause these kinds of symptoms.

I've also seen a bad 5101 cause these symptoms, as others mentioned.

That is a good point. The fish paper insulator behind the start button should be checked as well.

I think you have a switch with a shorted diode somewhere.

Couple of options...check the diode on every single switch in the game for shorts (a drag), or video the gameplay and capture when something weird happens (easier). Much easier to narrow the problem if I can see a video.

It could be any of those things but don't look past a faulty capacitor on one of the tilts aka (door, playfield, cabinet) I would put it in switch test and slam the game around. I would also cut those little caps off the fore mentioned switches. The key for me is when it's skipping a player. It thinks it's tilting and thus skips a player. Todd Scott

Not a dumb question. Yes, in diode test (the --|<-- symbol) you can test in circuit. It should read about .500 in one direction and infinite with the test leads reversed. If you get a steady tone the diode is shorted.

It seems random, but it's not. With a shorted diode it takes a specific sequence of 3 simultaneous switch closures to cause the MPU to think a 4th (undesirable) switch is closed. Typically, certain drop targets account for some of the closures.

Exactly, the outhole would be the 4th switch. Every one of the symtoms in your original post points to this type of problem.

You'll need to set the sound option again (gets "reset" to default when you remove the batteries or change out the 5101). You'll probably want to set it to "03".

From the manual..
embryon_sound.jpg

Yeah, when you first start with the Bally machines the sound thing can really throw you. Once you know though, you're good for next time

embryon (resized).jpg

I believe there's a matrix switch piggy-backed on the flipper's EOS switch that activates "FNIP-Save" flipper. Make sure those two switches are isolated from each other.

Put some insulator between that switches' contacts and see if problem remains/changes.

Looking at the switch matrix Vid posted and your description of what's going wrong, you've got some switch ghosting going on between the ST0 and ST1 signals. When the switches on strobe ST1 are closed, they're being shadowed to the switch return lines on ST0.

When you checked all the switch diodes, did you also check the diodes in the cabinet/front door switches (tilt/slam/start/right flipper)?

I've added the cabinet/door switch details (in red) below to Vids switch matrix to fill in the gaps. Note even though the right flipper button is in the cabinet, it's wired as a playfield switch.

Embryon_SwitchMatrix_All.jpg

Which matrix switch are you referring to?

According to the diagram above, it sounds like you have a shorted diode on coin chute 2.

Actually the coin chute switches don't have diodes. I should have removed those diodes from the coin switches on the diagram.

To the OP, does the problem occur when all drop targets are reset in the up position?

Put the game in switch test and raise the flipper by hand. Hold it up. What does the Credit/BIP display show?

[edit] based on the following post, ignore this one.

That second stacked switch on the main flipper EOS switch activates the upper right flipper and actually isn't part of the matrix.
Sorry, I wasn't clear about that above. The matrix switch for the right outlane flipback flipper is actually the second stacked switch on the right cabinet flipper button. Check the diode on that switch. The schematics say this right cabinet flipback flipper switch is wired to the playfield switch connector (J2) at the MPU board, not the cabinet switch connector (J3) at the MPU board, but anyway.

As you may or may not know, the switch test in service mode will only show the lowest logical switch number that's closed, i.e. if you press and hold the "A" Rollover, the player displays will flash "12", but if you then drop the ball in the outhole, the player displays will flash "08" and the closed "A" rollover switch "12" won't be displayed again until you remove the ball from the outhole.

So with this in mind, going through the switches backwards, can you try this when you get a few spare minutes:
1) Make sure all drop targets are reset up. Remove the ball from the outhole.
2) Go to the switch test in service mode. The Match/Ball In Play display should show "0"
3) Activate and release one switch at a time starting from the highest number switch working down towards the lowest number switch. When you get to the drop targets, drop one then lift it and move to the next.

Does any switch report the wrong number in the player displays when you close it?

See the attached diagram showing the switch numbers in Blue. Highest logical switch number starts at the bottom right corner and finishes with the lowest switch number at the top left.

Embryon_SwitchMatrix_ID.jpg

If it had a diode the switch would have to be stuck closed AND the diode would have to be bad to exhibit this problem.

Without the diode it's even better. Check to see if coin chute #2 switch is stuck closed.

Yes, a coin chute 2 switch stuck closed would explain the behavior and will show up in the switch test as closed with the ball removed from the outhole.