I know you said you overhauled the freewheel but...
I was about to start exchanging parts on my MV to get to the bottom of a grinding sound. I even contemplated getting my rear derailleur hanger checked, ...because I had done EVERYTHING else.
Finally I went crazy and opened up my freewheel to realize I was missing a couple bearings in both of the races. All is good now. If I go really crazy, I'll order a jar of bearings and replace them all so they match.