The Asetek water cooler uses a 3 pin fan connector that control the pump and both fans. This is the only connection on the board for the setup. The pump has a double 4 pin cable that the fans connet to and a USB cable that connects to a USB header which the software uses to monitor the fan speed and all that jazz. Asetek is the OEM that different companies rebrand as their own (Intel, AMD, Antec, Corsair, etc.). The setup is the same as this Antec kuhler water cooler (http://www.antec.com/download/Kuhler%20920%20Manual.pdf
The chassis fan headers on the Formula-Z that I connected it to after the problem are 4 pin. I think this evening I'm going to set it all up on fan headers with the pump connected on it's own then use a y-cable that came with the fans so they will not be powered from the pump and tell the BIOS to ignore the CPU Fan readings to hopefully get it to boot.
I figured I might as well test it all as much as I can before receiving the Advanced RMA replacement board.
My best guess is that I somehow connected the 3 pin connector from the radiator on to the 4 pin CPU header incorrectly. I remember reading of other people connecting 3 pin connectors and thinking, "How is that even possible? It has the little guide to make sure you plug it in right!"