Have you recently adjusted the CO levels or otherwise affected the richness of your air/fuel ratio (or even dirty air filter?).

I mention this because I asked my mechanic to try to get rid of the jerky throttle issue and he played with the CO level and made it very rich (put it to 30) - which helped with the throttle, but I noticed that the vibrations were much worse. I remember (when new) being able to comfortably hold 70km in 3rd gear (XT660X), and after he changed it, it felt awful - harsh anywhere above 60km in 3rd.

My handlebars and fairing would visibly shake (you could feel each detonation) at mid revs under acceleration - I couldn't get anywhere near rev ceiling.

I adjusted CO back (to 3) plus put stage 1/2 filters in (so much more air/leaner) and it is much better. The engine revs much better now - I can hold 70km again in 3rd. I fitted Kevs fuel mix resistor/gizmo but have wound it back (from Kevs recommended settings) to be leaner.

I find (on my) engine, it revs much more freely on a leaner setting.

I should say that I have also fitted Kevs other gizmo (sorry, it's been a few months - bad memory) which fixes the jerky throttle - whether that makes things richer all round (and I'm not running as lean as I think), I don't know. Basically I have leaned it off to where (I feel) it spins freely - the exhaust colour is still good so I am confident I am not running it too lean.

I got so conscious of the vibes, that I could tell the difference between fuel qualities (the vibes got worse on higher octane fuel). I've just set it for 98 octane and only use that now (worried that it will be way too lean on 90 octane).

Sorry for the long reply, but it was a very frustrating issue, and I was soo happy when I was able to resolve it. Hope it helps.