...Yamaha white plug on the left hand side of the fairing?
Had this issue with my 5PW R1 recently, it was in quite a state, then yesterday, about 1 minute after the bike having been fired up from cold, the cooling fan kicks off.
Obviously, no guage to go from, so I turn the bike off, get ready to ride off and re-start, 20 seconds later, no fan.
Wonder if it is just a crappy connection causing problems?