Couple things (from a non-mechanic)...
- if your oil is too high (and take it you checked with the bike level. A 2x4 under the kickstand gets the bike almost straight up) not only will some drip from the vent tube but you'll get oil in your air filter boxes. Good to check them (you have to take off or loosen the lower cowling to take the boxes off)
- coolant bottle should be be checked with the bike up straight. Good to do it when you check the oil level
- 6,000 miles in 2 years? Fan shouldn't come on with only a 12 mile ride unless you idled for a long time with the choke on before riding out. And if you rode with the choke on the mixture would be different and I would think make the engine run hotter. Being in Tennessee....you should be out riding more !
After checking the above mentioned items, go for another ride and see if things are running hot again. If it is...I'd agree with Bob...you are within your warranty so let the dealer figure it out.
Comment that others could talk about....if the bike is running on three cylinders, would the bike run hotter than normal? 3 cylinders doing the work of 4 ?