Sorry. I generally try to nudge people in the correct direction rather than being explicit about it. It is much more rewarding when you figure it out for yourself (with or without a nudge) than to be pointed directly. Some people don't care for it and prefer to be given the fish rather than learn how to fish. I can never tell but always default to thinking that people would rather learn how to fish. If you didn't want to learn then you should just pay a repair technician to fix the board.

Plenty of things could be failing. That's the diagnostic challenge. Finding where the failure is. If you expect someone to say "I've seen this before and it's obviously this" then you should send the board out for repair. Think of a non-functioning board like presenting to your physician with "I have a headache". If your physician says "I've seen headache before and it must be a migraine" then go find another physician. There are a myriad of causes for headache from simple stress to metastases. It needs to be investigated.

The pin will only start pulsing if the software is updating the display. I believe this happens during the ISR. PA2 of the display PIA is part of the 4-bit number for the digit strobe. The software has to strobe all 16 digits to produce the correct result on the display. It must strobe then CONSTANTLY. Hence, the software must be executing.

Your board falls into the category of "no boot" at this stage. You might think it has started as the LEDs blink. That's true. It does execute software. It just doesn't execute the main loop of the software. The processor works. It is either reading the wrong code to execute or the code is reading the wrong data and executing incorrectly due to the invalid input. Unless you put a hardware debugger on the processor, you won't be able to find out what the software is doing. It actually doesn't matter. Your board does not work properly.

Somewhat related, the thread @ https://pinside.com/pinball/forum/topic/i-fried-my-system-11-cpu-board-now-what describes a diagnostic and methodical way to process these boards. The cause for the circumstances are different but the net result is the same. Your board doesn't work.

My suggestion for the next step is to use the Leon to ensure that all the PIA ports are operating correctly. Make sure that you test the input port of the switch PIA as well. Right now, you don't know if the PIA is behaving incorrectly and causing the software to "crash" which results in the enabling of the blanking circuit.

When dealing with boards, always suspect prior work. Even your own. In your image above, it looks like someone has done some work with IC11 - the switch matrix PIA.

If you want better advice, post a well illuminated and in-focus image of the boards. Both boards. Both sides.

Otherwise, start probing around. Use the schematics as a guide as to what should be connected to where.

This shows that IC18 (PIA ports A and B) are functioning.

Yep. The problem is not IC18.

OP: Here's a suggestion that seems to have been overlooked.