Do a search on here for Fullsac. What you were probably experiencing in traffic, while stopped, was the bike going into it "heat control" mode, where it runs on the front cylinder and the rear one shuts down until you give it throttle to move, then fires back up. The bike runs very lean from the factory to meet EPA standards. While the ECM is able to adapt to small changes...perhaps to your V&H Slip On mufflers, it is possible that it made the air/fuel mixture even leaner, which is not a good thing. IMO, one of the simplest "fixes" for this is to put Fullsac's header pipe on the bike, thus getting rid of the catalytc converter, which is a source of a lot of the heat you're feeling on your leg. Hopefully, you were not wearing shorts, for a number of reasons.
Fullsac also offers the TTS Mastertune with some "canned" modifications to the air/fuel mixture...there are SEVERAL different products to alter the stock air/fuel mixture...that is really the only way you're going to cool the bike down some. Even then, you're still sitting on top of an air cooled, big cubic inch engine, so it's still going to be hot in traffic, and IMO, removing the lowers is not going to help in those situations. There are a brazzilion threads on the various ways to modify the stock exhaust system and the ECM.