A large difference between cylinders may indicate it is a good time to do a valve adjustment.
Other factors that can effect vibration are the weights on the ends of the bars. When installing hand guards it is important these are not removed or are replaced with equal size weights.
Kawasaki also reduced vibration with redesign of engine mounts and other related parts between Gen 1, Gen 2 and Gen 3 of the Versys 650. Also engine vibration is most pronounced around ~5K RPM so ideally it is best to shift down to avoid cruising for prolonged periods at this RPM. IMO the Versys has considerably less vibration than most other bikes I have ridden, eg. the Yamaha FJ09. A gen 3 Versys should have practically no vibration if it is running optimally. I have the same gen 2 bike as you and do not get hand tingles which can be an issue for me on other bikes I have ridden. Also ensure you do not have a death grip on bars, a secure but loose grip is ideal. Also is front wheel balanced?
Don't have much time now, so have to answer quickly.
First, many thanks for that excellent explanation re: throttle body sync. I did have a 7,500 mile service done earlier this summer, so perhaps it was included then, but not sure (can easily check).
I don't have aftermarket guards. Haven't changed bar ends and believe they are stock from first owner. Was considering getting heavier ones to alter vibes.
Surprised to hear that vibes are better than FZ-07 or FZ-09 since I've read so many comments about counterbalancing. I have read that the MkIII Versys is essentially vibe free after the additions Kawi made to the MkII.
I naturally maintain a very light grip with both hands. Seating position on Versys for me is excellent, so no need to lean on wrists and don't naturally grasp the grips hard. In short, this isn't the problem.
Re: front wheel balance... Had Pirelli DRIIIs installed earlier this season at the dealer, so expect balancing was done properly, but I suppose you never know.
To be clear, I find this uncomfortable after hours of riding. My typical rides are 3-4 hours long, sometimes with short breaks. I'd still like to get my bike to the equivalent of the MkIII, if possible.
Perhaps I am just "sensitive" after all.
Thanks so much,