I just re-read your comments and since my first response to you a few months ago. I have since found and cured the cause of the excessive vibration you are feeling between 2700-3200 RPM. It is the clutch basket (chudder). You will need to replace it with a modified unit to remove those vibrations. Of course poorly sync'd throttle bodies can add to this issue as well.
Originally Posted by brianjonesphoto
Ok guys I need some background. My 03 Vee sidecar rig does not have any aftermarket tuning equipment on it, but I could have been teka or yosh tuned. I don't have any off idle problems or noticeable surging. It does have the rough under throttle under 4K that is worst from 2700-3200.
The problem is Suzuki's poor design causing too much movement amongst all the parts that make up the basket assembly. As the miles add up these tolerances get bigger to the point of causing the issue you and I have experienced. This is a well know issue with the V Stroms' and Suzuki has never really addressed the problem.
The solution is to get in touch with Werks Parts, LLC and either make arrangements to have your baskets modified to fix the issue or buy and exchange unit. Terry the owner is on this forum often and I can tell you from my personal experience his work is a sight to behold, besides it works miracles to smooth out the Big Twin.
Terry also has a Youtube video showing step-by-step how to change out the clutch basket, if you have GOOD mechanical skills you should be able to do the job yourself as I did.
Here is the link to Werks Parts, LLC: https://www.werksparts.com/
Give Terry a call he will be happy to walk you through what he has done to fit Suzuki's piss poor design.