That happens when the piston outgrows the cylinder, it will scuff next to the wrist pin. It is possible that the clearance was too tight to begin with but usually high combustion temps are the cause. It is easy to run the main too hot if the pilot/popoff is very rich. This is common with "reverse jetting", everything is fine until a long full throttle run. If the pilot/popoff is set for cleaner part throttle you will usually have a hesitation indicating the main is too lean. The rear cyl is hot on Yamahas so open the top screw an extra 1/4 turn more than the front.
A month ago, I did notice the motor running rich by the look of the spark plugs (very black on the ground electrode). At that time, spark plugs were going bad unusually quick. I turned back both pilot and main jets just a tad and since then the new set of spark plugs have been clean and the right brownish color.
When I replaced the jets after putting a bpipe and a ADA head, I left the stock pop off springs if that matters.
Again, I have always been happy with the performance of the motor. The first time I took it apart was just to replace the wrist bearings as a regular maintenance and the second time I took the motor apart was because I sunk my ski.
I may have done a few full throttle runs but for not more than 20 seconds.
I run dual cooling if that also matters.
