Hi Rob,
Glad to help out. It would have been great to see both pinballs in action at the same time.

Did you get a chance to have any games on it today?

If it is still jumping the ball count, you could try looking at the following switches on the motor.

Motor 1C Normally Closed White +Blue / Blue + Black wire
Motor 2B Normally Closed Black + Yellow / Blue + Black wire
Motor 4C Normally Open Brown + Black / Blue + Black wire
Motor 4C Normally Open Orange + Black / Blue + Black wire

Check if they switch from open/close (or close/open for the NC) when you rotate the motor and give each a clean with the flex stone. If one of these is not gapped correctly it might be causing the ball stepper unit to advance one to many positions.

Regards Derek