Ditto on the boots thing. I wear tall Red Wings 99.9% of the time, high top hiking boots the rest of the time. I even prefer pull ons over lace ups so getting the laces caught isn't an issue.
Where I get the bothersome heat is on the inside of my right thigh. It doesn't have to be that hot out for it to be an issue, and trailing throttle conditions, i.e. going down a mountain pass, or slow traffic are the worst. It really isn't like the engine heat per se like you might feel at a stop light, this is a burning of the leg that can't be ignored. Originally my early Rocket had a bogus tune in it and installing the correct one made a big difference in the frequency this issue raised its head, but it still does happen.
I find it interesting (and encouraging) that many people report no issues at all with the heat, 'cause I'm not talking discomfort, I'm talking pain, whether wearing jeans or my leathers. I know it's bad enough on my bike it is a big reason I keep my Victory for my bagger - I simply don't want to deal with the burning leg thing when I'm supposed to be enjoying myself on tour.
Some of the things that are supposed to help with the heat are the correct tune, Rivco exhaust flange covers, freer flowing exhaust, header wrap, or maybe ceramic coating. I wonder if using a Tune Boy or PC111 to richen things up would also help?
FLT40, were you able to put your header heat shields back on after putting the header wrap on? My quick perusal of the situation indicated that may be a problem.