Find someone in melbourne (a member here on the forum) who has a Twilight Zone and go and have a good look at their wiring and take a camera or a video camera.
All it takes is 1 x wire to be off, or soldered on wrongly and u will have problems galore.
Also, i am not sure whether all of your boards have been tested properly or not ( I dont know what experience u have) but it might be time to call in a member/or a pinball tech who knows the Twilight Zone machine well, and get these annoying problems sorted out. Check every board after u have looked hard at all the wiring harness.
If u were in QLD, it would be a walk in the park, I know of 2 x techs who would help u for no charge, but u are in melbourne.
I reckon check someones wiring harness closely on their TZ and go from there.
C'mon guys, who in Melbourne can help this member out.