A lot of heat gets to the seat due to hot air exiting the two frame openings around the rear cylinder head (shown in the photo above). In some ways, the right side scoop makes this worse as it forces more cooling air across the rear cylinder head, a lot of which winds up flowing under the seat. (Note that this problem is apparently absent from bikes with the tall seat, probably due to having an extra ~2 inches of foam between your butt and the hot seat pan.) Not only does the hot air heat the seat, but the hot air blows out of the gap between the sides of the seat and the frame rails, especially on the right side. THAT can cook your right thigh. The other part of the comfort kit, the duct shown just below the rear shock upper attachment point, funnels the air from the cooling fan downward which keeps that air from blowing against the seat. When the fan kicks on, I think most of the air exits this way but by that time the seat's already hot. Note that this may be less of a problem on 08-up bikes with the revised ECM flash that keeps the fan running when the bike's above ~15 MPH.
At one point I modified my Uly by taking adhesive-backed aluminum HVAC tape (the stuff's that's made out of aluminum foil, not duct tape) and sealing those two frame openings off. That forced all the hot air to go through the fan duct and kept the seat noticeably cooler. It also completely eliminated the hot air that blows out between the top of the frame rails and the seat.
Unfortunately, a few months after I made the modification, I had a problem with my 77 connector (charging system); this resulted in the bike dying at interstate speeds due to a stone-dead battery. I played with the connector and jump-started the bike; apparently the charging system worked for a few minutes and then died again. The end result of this was the bike stopped twice when the engine was very hot and the cooling fan was unable to kick on to keep the rear head cool after the bike was shut off. About a month later I developed a rear rocker cover gasket leak.
The bike was still under warranty, so I removed the tape that sealed off the frame openings and I never put it back. I was a little worried that sealing off these two openings had significantly reduced the airflow over the rear head when the cooling fan is not operating, and this had contributed to the rocker cover gasket failure. I've never put the tape back.
After commuting during a couple of 90+ degree days this week, I'm about ready to re-do my modification. I think I'd be willing to rotate the engine and replace the gasket once in a while (if that's what it takes) if I could keep the seat 20 degrees cooler.
2007 Buell XB12X Ulysses
1983 Honda VT500FT Ascot