This is 'interesting' tp say the least !!

You have to start somewhere .
To eliminate the ignition system swap the ignition lead and spark plug from the good cylinder, I really don't think it's the problem, but you're just trying to eliminate possibilities now .
I would remove all the valve train parts on the affected side and give them a good inspection .
I had the rocker arm bearings fail on my '81 R65, the sheet metal shell broke out on the flange that hold the needle bearings in, I found several needle bearings missing on those bearings, but I also found the chewed up parts in the valve cover, again I don't think this is the case here .
If you don't see anything wrong, I'd swap in parts from your spare engine and see if anything changes .
By chance if you didn't know this, the rocker arm shafts have a drilled oil passageway .
It's been over 10 years since I had the head and cylinder off of this bike .
Oil supply for the rocker arm parts comes from I believe the lower cylinder studs, the corresponding hole in the shaft has to be on this stud, facing toward the cylinder head not the valve cover .
Hope that made sense !!

Did you have the cylinder off during your major work ??
Did you use any sealant in the area of the o-rings on the engine case where the lower cylinder studs come out ??
There's been a few reports of clogging the oil supply to the valve train parts because of sealant used in this area .
I don't know if any of this will get you closer to a solution to your issue here .