Turns out it wasn't the power supply after all, about 2 hours after I put the good power supply in it up and died again. And this time I could see that it was neither heat nor power that where the problem. Nor would it boot even after cooling down.
So today, I pulled everything apart piece by piece to find the problem. And at the core I found a horror. Some thermal paste had leaked down from the top of the CPU into the CPU socket. Apparently some had worked it's way dowm from the top before it had set up into a thick enough state, no telling what kind of damage this did to the processor or the motherboard but they both seem not to work properly.
I rebuilt the system with my old motherboard and 1.1 Ghz processor that I had been planning to use for my second machine. Which is how I am posting now.
I tried using the 1.8 Ghz processor in the old motherboard and the old 1.1 Ghz processor in the new motherboard, neither combination would work. The motherboard seems to be fried, unable to even try and boot correctly.
Putting the new chip in the old motherboard worked a little but was very unstable. I think I may be able to salvage the old processor if I can clean it off properly, though how I am going to get thermal paste of the pins I don't know.
Jay