I didn't think that it was an issue of weather the stock mufflers would fit the headers or not, I believe the issue is that the left stock muffler is more restricted than the right. You don't want the front cylinder having too little restriction in the right muffler, and the rear cylinder having too much restriction in the left muffler.

 

My passenger complained about the heat on my '08 Ultra also. I have since put on HD's heat shields, V&H's True Duals with the stock mufflers, racing tuner and tuned on a dyno. Passenger very happy with results and runs good.