I have an '07 Ultra SE witht he 110", and now an '09 with the 110".
When I first bought the '07 one of the first trips I took was riding to Vegas from Fresno. My bike did the exact same thing; went into Vegas traffic and immediately started making a racket with no power. I found out, that clattering is the engine going into "limp" mode, which it is supposed to do when overheating.
I came home, installed Bub Rinehart headers, a race tuner, then installed cooler burning plugs. Also, most important, when riding in anything other than really inclement weather, I remove the leg fairings and those tinted side fairing wind deflectors. Both of those really block air circulation. Doing all these things, I now have 10,000 on the '07 and while it does run a bit warmer than the 103", it gets nowhere near as hot as it did that day. Even in winter when I put the leg fairings back on, the bike gives no hint of overheating. I have had the bike in only once for the gasket recall, otherwise it has been excellent. Also keep in mind, as the bike gets more mileage (over 1,000), it will run cooler yet.
Don't worry, take a few steps to help it run cooler and you'll be a happy camper.
Wade aka torque