Where is the fan ground connected to?
Also, you might try just hooking up a few wires at a time, just power and ground first and get the basic fan function working, then add one extra wire at a time. I wrote up a little page on how I set up my Flex-a-lite fan controller:
http://www.4crawler.com/4x4/CheapTricks/WaterProofing.shtml#FanControl