I would ask if they, the service dept., have a yosh or tekka box. If they do you might want to consider working an adjustment into the deal. The adjustment should be at a later date though. My Strom was quite rough running when I first got it. After about 2k it smoothed out very well. At that time it was very easy to feel and hear the lean spot.
You might ask them to redo a TBS, throttle body synch. Only if you are not planning on any maintence yourself in the future. If you are going to be wrenching on the bike, do the TBS yourself, it'll get done and be right then.