This happens when you remove the connector to the coin door interface board. This is where switch #24 is located. When the game can't see switch #24 as closed it assumes that there is something wrong with the +12VR. This should disappear when you reconnect J212.

Consider disconnecting A-16807 - the "Custom Opto SW10 PCB Assembly". Reconnect your CPU connectors (J206 and J208) and disconnect J5 on A-16807. This will isolate the opto board. If the source of the ground short is on the board it should disappear.

Disconnecting J205 won't change the situation. Those are a bunch of orange wires that are direct grounded switches - not part of the matrix. You need to disconnect J5 on A-16807 - NOT J205 on the CPU board. This will isolate the A-16807 board from the switch matrix. If the source of the ground short is from the A-16807 board then it should disappear. J5 is a bunch of mostly white wires, some green wires, a black wire and a gray wire.

No. See the above. Disconnect J5 on A-16807 while leaving all the other connectors on the CPU board connected.

Yes. I'm overly cautious and I usually like to be 100% sure before proceeding. If I were doing this diagnosis I would disconnect J5 and see the problem disappear. Reconnect J5 and see the problem re-appear. Disconnect J5 again and see the problem disappear. Doing nothing else to the machine and seeing that kind of result leads me to conclude the problem is on the A-16807 board. That's a custom 10-opto switch board. You CANNOT replace it with a generic 10-opto switch board from another machine. This one for TZ was only used in TZ.

If you're comfortable with PCB diagnostic and repair I would bet that one (or more) of the LM339 ICs on the board is bad. You can purchase one @ https://www.pinballlife.com/10-opto-replacement-board-for-twilight-zone-a-16807.html if you just want to replace the board with a new one.

The old board can be repaired. I would not throw it out. If you decide you want to throw it I'd be interested in it.

The ICs were NOT socketed from the factory so someone has done some work on that board. Check the previous work to make sure that the circuitry (continuity) is correct.