First concentrate on one problem at a time.

If the 2nd ball gives double bonus and the 3rd ball in a 3 ball game also gives double bonus, diagnose this circuit with Alligator clip jumper wires, especially the 3 indicated areas.

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Check the end-of-stroke switch on player 2's 1000 score reel

Check the 9th position switch on the 1000 score reel of the player that's acting up.

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If the Add Player Unit relay (P) doesn't activate the Add Player Unit solenoid, Inspect and diagnose this circuit with Alligator clip jumper wires
http://www.planetimming.com/Pinball/troubleshooting/EM%20Troubleshooting.pdf
http://www.pinrepair.com/em/index3.htm#features

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If the replay button activates the Replay Button relay (V) when there are already 2 players, one of these switches is closed when it shouldn't be.

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Which of these switches is making the score motor run?

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D is the Yellow Hole relay

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I asked which switch is making the motor run and you answered "D ...". I don't think it's the Yellow Hole relay. So I'll ask again, which switch is making the motor run continuously?

Or if you'd like to try a phone call, send me your cell # in a private message.