Is the interrupter underneath in good shape? Does the trunk stop turning when you hit the trunk while its turning?

Check where the set screw is, if it's cracked.

Then in trunk test see what it's opto is doing.

LTG : )

I would sincerely look at getting one of the new boards that removes that bug. I purchased these for my ToM that's on route. I couldn't imagine trying to route it without it. Price went up a bit, but welcome to today's economy.

https://www.tanglestech.com/TPP-1039

I also had an Ingo board in the last ToM I had, that worked great as well, but I didn't get a response on that thread when I inquired about getting another.

You don't need all three unless your outlane magnets are giving you trouble

Can't say I recall experiencing this bug, but perhaps it comes down to the ROM version? There is a version 1.3X patch F0F8 ROM for Theatre out there that has the following tidbits in the release notes:
"The Trunk error handling procedure has been refined to not give a false positive during normal playing conditions with a healthy Trunk mech.

With secondary function to reset the error state in case of genuine in-game Trunk error (stock ball).
When tournament play selected: Opening/closing the coin door will reset the Trunk error state."

The ROM is part of the PinMAME romset

Don't try to fix it, there are good new cards around that basically change the logic of the trunk opto (which is deficient on multiple fronts) and remove all the errors. Also buy yourself and unbreakable trunk in rubber you won’t regret it.

https://www.ministryofpinball.com/en/theatre-of-magic-trunk-opto-board.html
https://pinside.com/pinball/forum/topic/unbreakable-trunk-for-the-theatre-of-magic