Running Hot?

[donebysunday]

stock

Ok, it's all stock. I was running it without the airbox though, in case I had to take the carbs out again.

That would make a little difference . I usually run without the air box for a very short time on clean roads (don't want to pick up road dust/sand) just to check the performance of the air flow through the box/filter .
Stock exhaust then ?

[mschor]

When you start using the choke you are introducing extra fuel to the engine. The engine may not be able to handle all the excess and some will burn past the engine and into the exhaust. The fuel burning in the head pipes will cause the head pipes to heat up nicely basically warming the engine faster. That is normal, typically these bikes are lean from the factory to meet EPA regs..
What pipes and air filters are you running ?

Yeah, the bike is pretty much all stock, the only mod I've done is the brake lines and taking out the octopus to run straight fuel lines. So far so good.