Have you tried resetting the cmos settings by removing the battery or with the jumpers ? If you can reset the settings, you might be able to build. I believe the problem is you did not lock the pci-e bus to 100mhz. If set to auto it will go very high. If this does not work, check out these motherboards:
ASUS P5Q Pro
So the reason the card is hot is that the PCI-e bus is very high? That makes me much happier than thinking it got more voltage than it should be.
Thanks for the reply!