Sooo... the bike has been running REALLY hot and the fan doesn't turn on. The radiator cap is venting coolant.
I have been looking everything over and what happened is that when I replaced the right head cover after checking the valves I got the electrical wire pinched in the cover. After looking at the service manual I think that this wire is either for the "engine coolant temperature" or the "thermostatic switch." Once my engine cools down I am going to pull the head cover off and inspect the wire.
Hopefully I haven't screwed things up too much...
