DZ,
I am dealing with the same issue. I thought by installing the Trident pipes and getting rid of the factory exhaust (it has two HOT catalytic converters in it) that it would get rid of most of the heat. Well, no such luck. My theory, for those of us who have the problem, is that hot air is flowing from under the gas tank and up under the seat. I also think that some of the heat is generated by the vertical part of the pipe (under the seat) migrates past the gap between the heat shield and the plastic battery box and adds to the heat under the seat.
I just recently bought some exhaust header wrap and covered most of the vertical pipe. It seems to have helped a little, but I still get a HOT seat. I am in the process of enclosing and sealing the bottom of the battery box and insulating it somehow to help reject some of the heat that I believe is sneaking up there. I also might try and fill in the gap that exists (pretty small really but it should help) between the gas tank and the battery area under the seat.
If you come up with a different solution, please be sure to let the rest of us here who have the same problem know! 
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Mods: Trident exhaust, GSG frame sliders, Stebel Horn, Homemade (OnD Style) Tidy Tail with Rizoma signals, Homemade axle sliders, Invisible bra paint protection, Red wheel stripes and Pazzo Levers, battery voltage indicator, SpeedoHealer, Hyperlites.
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