You can only feel it in the bars, not the seat or anything else? Can you duplicate it standing still, in neutral, and holding the rpm's at 2500 to 2600? Has anyone checked the torque on the mounting bolts for the handle bars?
If it does it only while riding, note how fast you are going. Then... try to maintain that speed and vary the gears you are using to maintain that speed so you vary the rpms. Is it really more speed based than rpm based? If so look at front tire air pressure, balance, abnormal wear, bearing play, steering head play ect....
If the only thing that that changes the vibration is pulling in the clutch, and it won't do it in neutral, and it isn't speed related, and all your bolts are torqued correctly, I'd almost have to say the problem is in the clutch.
Another thing... maybe you could ride another Rocket and see if that one does it. Its gonna be a crappy weekend here or I'd go out and try for ya...