1-9 sequence is controlled/ advanced, by a stepper unit on the back side of the play field. Check the operation of that unit, likely the problem lies there. You may need to trace all related circuits that control that unit's advancement. Hopefully you have a schematic, if not, will need to get that-PBR has them.
If the ball gets caught behind the drop targets, try adding a second set of rubber on those posts (there was a recent thread about that here in the EM club house).
Special lights will not happen if the game does not get thru the 1-9 sequence, so yes, related to issue one.
Match unit (located in the back box) can be finicky, you should examine it to make sure this mini-stepper is advancing each time it should. (can't remember if it's on ten point scoring, etc.) Again, see schematic for the full control circuit. Hope that gives you a general idea of what to look for. Great game-when it's fully functional! Report back with your findings and others will also have ideas for you.

I think you are talking about the score motor isolation plug. Can be used to disconnect the motor while the game is on if you need to service it. There are a few things that can be checked in that state. Yes, just trigger the rollover switches to test the advance. The two star rollovers should alternate, so one or both need adjustment. They control the three stand ups next to the bagatelle lanes. Important to have those working to advance the sequence (also score specials). Beyond cleaning those steppers, make sure they are working correctly (contacts aligned) and no wires broken, etc. You'll get there.