[Water Warrior 2]

Gotta agree with ER, the bike isn't going in and out of gear. If it was there would be more than enough noise and clattering to get 110 % of your attention. I think if there is a surging it would be electrical or fuel related. Check the lines at the fuel cock. 3 lines, 2 for fuel and one for the vacuum operated diaphram. Make sure none of them is pinched to restrict vacuum or flow.
Also keep in mind that the overall load on the engine in a taller gear may find the weakest part in the ignition system and lead to a surging issue.
Now, about that shifter. Check over the shifter and all pivot points. Make sure all adjustment points are tight. If memory serves me correctly there are 2 little Hemi joints inside rubber boots that should be lubed every so often. Just give them a shot of chain lube inside the rubber boot. Works like magic on the Vstrom.
Not going to go back to reading previous posts so tell me. How old is the bike and how many miles(kms). Have a thought to dwell upon.