I had the same problem after rejetting. The wire conected to the sensor fell off when I fliped my card over. Check the wire and make sure it is still conected to the sensor located on the back side of the head (if you already haven't).
If you already haven't place a positve feed on one end of the feed coming directly from the fan and the other end to a ground. If the fan doesn't work I would say the fan motor is bad or wire conections to the motor are bad.
If it works I would follow the Wiring Diagram on page 25-3 in the owners manual. Set a meter to OHms and test each wire conection. This will tell you where the conection is failing.
ROC i just did that and the fan kick on and worked fine. I also traced every wire on the bike and they all conect wothout any damage to them. The only other thing i can think of is the thermostat but i dont no how to take it off or where its at.
I have a 2004 rincon. the fan is not working. I have replace the coolant temp. sensor, the oil temp sensor, checked the thermostat in boiling water works fine and replaced the fan. still getting an overheating light and the fan not working.