Hi Mad Dog,
Excuse my ignorance (I am sure someone will tell me if i am wrong) but my 999 got very hot in the summer. I spoke to pro twins and they told me that most of the problem was due to the catalytic converters (they only operate at higher temperatures) and that the best way to solve it was loose the cats.
Mind you it was probably Brett trying to flog me a full leo vince or termi system being closer to the truth.
I dont know if you have catalytic converter on your bike, if so where its mounted.
Just a different angle to look at it from maybe?