as far as you know.
Have you bothered to replace the CPU card with another 604/e/ev to see if it's the CPU Card?
I have a spare daughter card that if you want to pay shipping, I will just GIVE it to you. Or for $7 I can ship you a 366-400Mhz G3 (I think) which is a MACh Carrier G3 Zif. That I know works.
for another $5, I will also give you the software for the G3 (which I paid close to $20 for OS 9/OS X Software versions)
I also have another PM 9500 board iirc, so that may get you up and running as well. I will have to check around, but I should also have the power supply from the machine. That would be another thing to check. Make sure the PSU is giving the necessary power. Test it with a multimeter and see if you have any dead leads. If you do, it may be that the CPU is not getting enough power and that could be causing the issues.
Another thought is that when I worked on mine, I found that the video card should be closer to the CPU and I had more luck with mine.
I got rid of the tower and stuff (except the electronics) because of the back falling off.
Let me see what I have. I will try to post more of what I can remember.
That PM 9500 is one TRICKY beast. I pulled more hair out with one of those than even a PC that I have had issues with!
IMHO, the 9500 was the WORST machine I have ever seen apple release in a desktop. The 7200 was better!