Heres how I found it..
2 tools needed. Oscilloscope & Schematic/Flowchart. Basically, i was getting no foreground objects and bunches of lines on the screen. I tried ruling out the rams, by disabling them by grounding out the enable pins.. I could make the lines go away, but it wasnt consistant.. I tried grounding out the individual ins and outs on the buffer ram, and I found that I could clear the lines bu grounding out the ram inputs. So that told me that the problem was upstream of the rams, and that nothing was getting written to them. The flowchart showed that the foreground objects basically get loaded from the roms through a shift register, a latch, and then into the buffer ram. I figured either the clock was missing or one of the latch chips was dead, because it was a wholistic problem, not a corruption. Using the schematic, I take the scope and start looking at the clock and enable pins, and its flatlined... So I followed the logic, and found an OR gate that had a live signal on the input pins and 0v on the output pin. I replaced that chip and it came up.
Kinda the same thing for the SSIO board.. I think the watchdogging I saw might have been something I had hooked up wrong.. but I actually started checking clock signals first..Usually when the whole board is dead I check the processor and clock first. Sure enough the clock pin on the processor was dead.. traced the circuit and found a logic gate dead..
BTW the spinner issue was I think just a dirty optical sensor. I replaced the 339 because I thought it was dead, but that didnt fix it.. I was getting 2.8vs on the out of one of the sensors and 6v on the other. After messing with it, I started gettign 6 on the first one, and 2.8 on the second..hmm... kept cleaning, and got 6 on both... I did resolder all the pins too, so could have been that too..