I'll have a stab at trying to piece your puzzle together. Right now I don't have a single point of failure that explains everything you've described but some more clarification may help.
First things first. Can you post a picture of the the switch matrix shown on the display when you enter "T.2" (switch levels). You can also use "T.1" (switch edges) if you like.
These are separate to the 10-opto board. The ball trough optos are handled directly on the trough opto board and are all in column 8. The flipper optos are directly grounded switches.
The idol optos are handled by the 3-opto board. They are in column 9 so they won't show up in any switch test so you cannot manually test them. You need to run the idol test. If the idol test passes then these are fine.
The POA top right switch is #75. Not sure how this relates other than the 3 additional optos handled by the 10-opto board are in column 7 but if you can verify that all the other switch in column 7 work then this will remain unexplained. If the other switches in column 7 do NOT work then you have a generic column error.
The POA entry post switch is #46. This is in the same column as all the other optos - column 4. The only other outlier is #48. This is the right slingshot. Please verify that this switch registers. If this switch does NOT work then you have a generic column error. Otherwise you can some other error.
Please post back the results. The goal here is isolate if the problem is on your CPU board or in the playfield wiring. You can instantly rule out CPU board by jumping (shorting) row pins to column pins in switch edges and verify that the switches register. Focus on column 4 and column 7. If problem appears to fall into "some other error" it may be a playfield wiring problem. These are hard to diagnose remotely because the problem often has to be seen in person and cannot be easily deduced due to the daisy chain nature of the wiring.
The only other relevant questions I can think of ...
- Did you acquire the machine in this state or was this working and then suddenly stopped working?
- If it suddenly stopped working what kind of recent work did you do to the machine - if you did something please be honest. We all make mistakes but without accurate information diagnosis is made much harder.