If you look up 1980s Yamaha Open Class bikes in the dictionary the first words are "jetting problems." It sounds like you have done your homework and tried most of the known tuner fixes. The first thing I would suggest is going back to the basics. Check the condition of your carb, the reeds, the engine’s compression, the main seals for leaks, the condition of the silencer, and the timing before you do anything. Next, I would look at my fuel mixture. Unless you are riding the bike in Baja at 100 mph, the bike is usually ridden at low rpm and best served using a 40/60-1 mixture of synthetic ester based oil. While I have heard of people giving up the old, round slide Mikunis for the Keihin carb from a KX500, I think you run into the same jetting go around as before. Finally, try giving Eric Gorr of Forward Motion a call. He has a lot of good tuning info on older 2 strokes.