Hi,
When you installed 3.9 on the fresh partition, this was before or after you made all the hardware changes? I'm sure you already have, but you've gone back inside the machine & pressed down firmly on all the chips, right? Have you tried running any other graphics software besides Cybergraphx? (And as a final thought, does anybody with more experience than myself know if the A3000 power supply might not be able to support all of these items?)
Good luck,
Mike