I know what you mean about the heat.
I changed the headers out to V&Hs Duels: I didn't notice much improvement.
I then had the bike tuned on a dyno with the Screamin' Eagle tuner: I didn't notice much improvement.
I change the mufflers to 4" Rineharts because the tuner said the stock mufflers were very restrictive: I didn't notice much improvement.
I then installed the Full Sac X-Pipe header
http://www.fullsac.com/x-pipe.html : I noticed some major improvement with the heat
(I did retune on a dyno with the new headers)
I then went with the 2" baffles from Full Sac in the stock mufflers because the Rineharts were 2 1/4" baffle and a little loud for my old ears
No change in heat, it was still a lot better but still noticeable.
I then installed Wards Parts head cooling fans
http://www.wardspartswerks.com/ : I have noticed even more major improvement with the heat
So I do recommend
Fullsac system and the Wards Parts fans.