borntoride - If your problem persists, you should be eligible for the upgrade kit since it was manufactured before 11/07.
A few here have had some teething problems, mine is currently getting the upgrade kit, replacing the head gasket and a new TDU, and my warranty was up in 02/08. All taken care of by Triumph. It has taken a few years for Triumph to get the bugs worked out, but they are obviously commited to the Rocket engine for years to come if they are still engineering upgrades for it. Daryl your bike seems like the perfect storm. I'd be upset too but give them a chance to get it straightened out and see if the bike can regain your trust.