I am home from work now, so I have time to comment a bit more now. The thread I alluded to above I like because he is having a similar problem to you, and a similar one to me as well.
The pictures are pretty good too. Some of the major points are hit by folks who have actually done the work.
This guys problem (in my opinion) was that he got his entirely our of whack trying to get rid of PTO grinding. We shouldn't have to get ours adjusted crazy to accomplish that. The best we can do is adjust it correctly. If there is another problem, we likely will not fix it with bizarre adjustment approaches.
Every time you stop your tractor by using the clutch, there is some momentum keeping the shafts turning, but after that is gone, you should not grind, or grind very little.
But how often do we really have the PTO clutch fully disengaged, and know the PTO is not rotating. In that state, any surface rust etc would be polished away. A fully engaged clutch does not polish. A fully disengaged clutch with the PTO free to turn does not polish. I think fully disengaged clutch with the PTO shaft known to be stopped will eventually polish things back up.
I think the inertia of a rotary cutter would be perfect to exercise the PTO clutch. Engage the clutch, then disengage, over and over for a little while.
Adjust it properly, it may be good. If not, exercise it. Don't stay partially engaged any longer than you ordinarily would while starting a high inertia load.
I hope this helps in the off chance that it still grinds a bit after being properly adjusted. Other than the exercise approach, all I'd know to do is split it. I've split a tractor before, and it doesn't terrify me, but I have things I'd rather do if possible.
