OK so I actually had some time today to look into this "correctly".
I may have been getting my Capcom machines mixed up. That said, I got the following on the Pinball Magic this morning:
Trunk optos - All register correctly, using an actual pinball.
Outhole switch - registers correctly using an actual pinball.
Shooter lane switch - registers correctly using an actual pinball.
Ball trough - Left and center register, right does NOT.
These are original Capcom opto boards which have had the receivers and transmitters replaced.
Troubleshooting - I had another capcom board (with only 3 optos on it) from before. It was not marked, so I don't know it's actual condition, but it yielded the same result.
I then replaced the transmitter and receiver opto from the "trought right" position on my existing boards. Same result.
So at this point I am guessing either one (or both) if the boards are bad (I did reflow the connector solder points), OR, I have a wiring issue.
Does that sound like the right track?
I haven't done it yet, but I can take the trough optos from my Breakshot and try them in my Pinball Magic. That would likely yield a more direct path since Breakshot is working.