The Vee (1000cc) is a vibey engine, uneven firing pulses are often cited as the cause.
Mine had a rough spot at 3500 - 4000 rpm, I had the FI set up and this really helped the vibes, I got used to the residual issues.
If it goes when you pull the clutch in , you pay have the clutch judder issue, search the forums for chudder.