Primaries always get hot. They're bolted to a hot engine and the heat transfers right to the primary. No problem.
Compared to my wife's '04 Road King Custom and my '03 Low Rider there is an extream difference in temperature. I could ride the '03 very hard in very hot temps and it was never as hot as the 110 CI.
In the earlier years the motors were not running as lean and producing as much heat. This heat has to go somewhere, and the heat in the bottom end goes into the oil and radiates out through the aluminum. Aluminum is a very good conductor, so heat in the crankcase is transferred to the primary and the transmission.
The charging system is also more powerful which generates more heat. Nothing on these bikes runs cooler than it used to, and all that extra heat has to go somewhere.
If you feel there is a problem, then I suggest you take it in to the dealer. Unfortunately, they will probably tell you "they all do it and its just something you'll need to get used to." Other than that, I don't know what to say to make you feel better.