Today I swapped the CPU cards and carefully reassembled my Quad. The system seems to be working and I feel like I just tamed four wild horses and got them to play nicely with each other in the same stables. I have been loading up the system, compiling binaries, compressing video, listening to music, playing YouTube, etc. but haven't been able to make the system thermally shutdown. See picture above. Temperatures on CPU B max out in the 70C range, then quickly cool down back to the low 50s when idle. Both CPUs are running cooler than on my air-cooled dual core G5. Fans are louder than I'd like, but they're not running full out either.
That being said, when I run thermal calibration, the system gives an error message that the maximum CPU temperature has been exceeded. I know this is not the case and unlike earlier attempts, the system doesn't shut down, it just gives me the error and I can either reattempt calibration or shut down. I'm not sure why calibration isn't successful. But at least now I have a 100% useable system. I'll let it cool overnight, and try calibration when the ambient temperature is cooler. But at this point, I'm inclined to say this project has been successful and I now have a reliable and useful G5 Quad. I have learned more about G5 quads and liquid cooling systems than I ever wanted to know and I can now think about upgrading the RAM, getting an SSD, better video card, etc.
I'll probably repurpose my dual core G5 as a server and play with OS X server over a network. I have a couple of older intel- iMacs that I can put Snow Leopard on and have a small vintage Mac home network.
Again: This is the best Power PC Mac ever made, and it's also the worst Power PC Mac ever made. Do not buy this computer.