I'd first look at why the score motor keeps running. You'll want to look at the circuits/switches that send power to the score motor.

One of the primary switches that sends power to the score motor would be a reset relay switch. When the score motor is running, is the switch on the reset relay (yellow wire and orange/green wire) opened or closed?

Also, check the target relay switch (yellow wire and orange/green wire) to see if it is opened or closed while the score motor is running, and check if the switch is adjusted properly. Check all the target switches on the playfield to make sure they are open.

And, make sure the B index switch (motor run switch) (yellow wire and orange/green wire) on the score motor is opening and closing properly.

Check the switch stacks to confirm there are no shorting wires or wire lugs. Make sure on the relays that are checked that the switch stack screws are tight.

The reset relay is energized, which is closing a switch that sends power to the score motor. Now we'll need to look at the circuits and switches that send power to the reset relay coil.

There is one switches that can initially send power to the reset relay coil:

Coin relay switch - yellow wire and blue/white wire

When the reset relay coil is energized, it will close a reset relay switch and it will enable five switches to send power to the reset relay coil:

Reset relay switch - blue/green wire and blue/white wire

1 point DU (drum unit) 0 (zero) switch - yellow wire and blue/green wire
10 point DU (drum unit) 0 (zero) switch - yellow wire and blue/green wire
100 point DU (drum unit) 0 (zero) switch - yellow wire and blue/green wire
1000 point DU (drum unit) 0 (zero) switch - yellow wire and blue/green wire
Score motor switch 4B (reset relay lock in) - yellow wire and blue/green wire

When the score motor is running, is the above coin relay switch open or closed? Also, check all the score drum unit zero switches. All these zero switches should be in the open position when the score reels are at the zero position. Is score motor switch 4B opening and closing as the score motor turns? When the reset relay is not energized (machine power off), is the reset relay switch open or closed?

If you find the coin relay switch is always closed when the score motor is running, then you would want to look at the circuits and switches that send power to the coin relay coil. Power to the coin relay coil is initially sent from the coin switch. You would check if a coin switch was stuck in the closed position...

It's great you found the problem! It's not that common to have a problem with a kick off switch, so this one was a little tougher to troubleshoot. Enjoy the machine!

Have you checked the plugs on the high score adjustment? Make a note of the how the high score adjustment is set up. Then disconnect all of the high score plugs from their plug jacks. Then activate the 100 pt relay and see if the ball count step up problem happens again.

It looks like you'll have to take a look at all of the circuits and switches that send power to the ball count step up solenoid. Since the problem only happens when the 100 pt relay is activated, I'd first try to block power that leads from the 100 pt drum unit. Try to block power using a piece of paper or tape between the switches at the white/green wire of the 100 pt drum unit.

Also, the problem could be related to the "aftermarket" wiring shown in the photo of post #2. You can always temporarily disconnect some of these wiring junctions to see if it will alter power to the ball count step up unit when the 100 pt relay is activated.

The green/white wire does go to a ground point on the 100 pt drum unit, but there is also a junction where the green/white wire branches off to a switch, which should be the switch blade that rotates on the 100 pt drum unit. This rotating switch blade contact can make a connection with 4th contact rivet and 5th contact rivet. If the rotating switch blade contact is not touching the 4th or 5th contact rivet, then power would not be able to reach the ball count setup unit solenoid via the drum unit.

You can totally isolate the circuit by blocking "gateway" switches from other circuits that connect to the ball count step up solenoid. To isolate the circuit, you can block the following switches:

Game relay switch - white/green wire and red/blue wire
Score motor switch C-IND (B) - white/green wire and orange/black wire

With these switches blocked with a piece of paper or tape, you can look at the 4th and 5th drum unit contact rivets:

100 pt drum unit contact rivet 4th - orange wire
100 pt drum unit contact rivet 5th - blue wire

You can cover the contact rivets with a piece of Scotch tape so the rotating blade contact can slide over the tape.

With all four contact switches blocked, there would be no way for power to reach the ball count step up solenoid. If the ball count step up solenoid still gets energized with all four contact switches blocked, then there would be a short in one of the circuits/switches/drum unit.

With the game relay switch and the score motor switch blocked, the 100 pt drum unit should only be able to send power to the ball count step up solenoid when the rotating switch blade is in contact with the 4th or 5th contact rivet.

You can experiment with blocking and unblocking those four switches in different combinations to see what happens. Example: Block three switches and unblock one switch; block two switches and unblock two switches, etc.

UPDATE: I didn't see the last post before posting... Looks like you found the problem on the drum unit switch - the ground wire was sending power to the ball count step up solenoid. An unusual problem - good job finding it!