A cunning plan
I am not a Yamaha expert, but if the valves have been run for any length of time with excessive clearance, then the tappet will hammer it's way into the top of the valve stem making it impossible as you state to accurately set the clearances. I would guess that the Yamaha engine uses a common rocker to open both valves, the easy way to check the problem is to set the tappets to very nearly zero clearance by releasing the locknut and screwing the tappet until it makes contact with the valve and then back off say an eighth of a turn and lock the nut. do the same for both exhaust valves. There would be no harm done if you set them to zero, but only run the engine for a few minutes, just to test. It may of course not be the exhaust valve, could be the inlet valves or even piston slap or cam wear. Short journeys are an engines worst enemy regarding premature wear.