When I bought my Rocket it was hard to change gear and find neutral, there was bad popping on decel with cat bypass and TORS, and the fuel gauge was not working - potentially the worst problem but luckily I twigged that it was doing to many mpgs even for running in and got to a garage just as it ran out.
The gauge was fixed and I was assured the trans would limber up - it did and is now fairly good.
I was fobbed off about the popping "It's because of the open pipes sir" they kept saying. "I've three other bikes with open pipes and none of them do it" I kept saying, to no avail, so I bought a Tuneboy. While I was figuring out what to do with it another tune recall came - I had it done and now it seems acceptable so I probably wont mess with it apart from releasing the lower gear power.