So I've isolated my problem, to having the 5v rail, go from 4.98 fairly steady, to 1v once plugged into the mainboard, nothing else is connected as I wanted to isolate the issue.
To step back, I re-did the caps (all of them) on the SDB about a week ago, and it's been playing fine for about a week (20 Games). Then Friday evening I put some Cliffy protectors in, all the hardware that came out, went back in, no surplus nothing missing. So I'm fairly certain it's not something that's shorting anything out on the board. Saturday Morning I come into the room, turn it on, and the GI lights are on, the DMD is dark, and I look behind the black glass, no diagnostic lights +5v etc..
So I turn everything off, and start reading and diagnosing, because I don't have any diagnostic lights on the CPU, I can't / won't get anything on the DMD, because it also has nothing to go off of, because it hasn't been sent anything. I remove all connectors to the CPU Board, and just connect the wires next to the battery tray, (Game is NVram so no battery leakage that anybody can see / detect). And power it on, nothing on the diagnostic led's.
I take the game out to hook up to one of my PC Power supplies 5v supply, and lo and behold it powers up, goes through diagnostic, and gives me two red lights. (normal)
So since the CPU is good, and tests well with 5v, didn't blow a breaker or anything for drawing too much, I focus back on the power supply, the odd thing is I haven't touched that thing in a week. Before then yes it had several old caps, so that's why I replaced them, I had a low 12v side @ around 10.1v, I matched polarity, and microfarads. Everything I was supposed to... and it ran...for a week, but maybe the new caps put stress on some of the other old components?
I just re-flowed the bridge rectifier, and still same sad story.
Any thoughts?