By your wording, it sounds like you've investigated, but-.......... (and you do mean FINAL drive, not Primary??)
If you haven't already done so, maybe employ a mirror to look along the chain, and up under(one of those oversize dentist ones from auto shop are handy), get it on the centre stand, remove the chainguard if necessary, and turn the wheel. you should hear/see something scraping.....??
Wouldn't a spacer(other than necessary for the natural gap) between chaincase and frame make it worse??
Isn't there a spacer between the inner case and crank-case? Maybe that's missing?? or maybe needs (thicker) one??
also check that the sprocket nut is done up tight, a loose one of those would allow the sprocket/chain to float over onto the primary...??
I had a similar but different thing, but it was the con-link had caught the corner of the chainguard
good Luck, cheers duTch