If the Coin Unit stepup solenoid doesn't activate when you push the start button for player 2, , inspect and diagnose this circuit with Alligator clip jumper wires, starting with this switch on the Reset relay.
http://www.planetimming.com/Pinball/troubleshooting/EM%20Troubleshooting.pdf
http://www.pinrepair.com/em/index3.htm#features

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Does the Coin Unit stepup solenoid activate when you push the start button for player 2?

If you'd like to try a phone call, send me your phone # in a private message. I have some time Sunday evening and probably again on Thursday.

I see that on the schematic. Next I'm going to review the way these steps are timed by the motor.

The Game Over and Reset relays shouldn't activate when you're adding the 2nd player. Do they?

I'm hearing that the Game Over relay trips then latches when the replay button is pushed for second player. Is that right?

If the Game Over relay trips then latches when the replay button is pushed for second player, check these 2 switches. They should stay open.

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Be careful before you reposition the ratchet. The Ball Count unit has a wiper that has to be positioned correctly. Here's a page from the Jubilee manual.

Also, the missing ratchet teeth have to be positioned correctly.

Ball Count wiper