Have you got the wiring diagrams and schematics?

The ones from http://www.firepowerpinball.com/  particularly the backbox wiring will help for interconnections and voltage levels and identifying harnesses.  I think I recall reading the GI wiring is run differently or fused in a different way on sys3 games, even though the power supply board is the same.

You should be able to do a fair bit of testing even without J2 as it is just the solenoid and lamp ground. The lamp supplies just passes through the power supply board via nothing other than fuse F3 and the solenoid supply  has a few soothing caps, a protection varistor and is fused by F2 on the power supply board.