IF... And that's a BIG IF... I wanted to make my R3 quieter and smother..... I would re install my stock roadster exhaust system and air intake system and have a complete NEW Professional dyno tune done.
BTW... What year and model do you have- its not in your "rides" description (makes it easier when asking help advise etc...)
I can't see any way that the stock exhaust on the Rocket can be described as loud. Frankly, I don't even hear it on mine once I get up to anything like normal speed, just a turbine-like whine from the engine. Granted, mine is a Touring but stock Roadsters are also quiet. Since it's a used bike, it probably has TORs or some other aftermarket slip-ons.
Some of them do tend to vibrate. Mine vibrates a bit more than I'd like, and much of it goes away when I pull the clutch in just a hair, so it's something in the transmission, others have reported the same. To date I have yet to hear of any failures because of it but it is a bit annoying at some revs.
Whatever vibration you feel isn't coming from the exhaust though unless it's literally flapping in the breeze. Iso-grips is one way to go, also look at the angle of the bars (one's wrists need to be as closed to the relaxed position as possible) etc.