On the other end of the scale, I have an early model (July '04) with 43,000 miles on it and have not had any mechanical issues at all. In fact my bike is running great right now..
As far as pipes, they are a personal preference. I have been running the TORs/cat bypass combo for a long time and I LOVE the sound of them, and the motor revs much more freely than with stock exhaust. However, after hearing Britman's Jardines at RAA III, I am now about $30 shy of pulling the trigger on a set of Jardines, probably next week..