reading your post I saw that you never mentioned anything about the carbs. I had the very same problem but it was on the left side. Come to find out the needle was bent and causing a disruption in the air flow so whe the spark plug sparked the fuel and air mixture was all fucked up not causing a good explosion when the plug sparked causing it to not fire right.. it would idle fine with both cylinders firing correctly then when I accelerated, it was like a light switch and the left cylinder would not fire but then right before red line of every gear the the cylinder would come back to life and the shee would scream, until you shifted and dropped the RPM's and the cylinder would shut off. I would also try to accelerate slowly and the cylinder would fire intermittantly until very close to red line and then it came to life and I had to hold on so I wouldn't get dumped on my ass. It was in the shop for 3 weeks and they fucked with it every day. The owner even got involved and so did just about every mechanic that got a call about the issues I was having with my shee. They tore the engine down all the way to look at the base gasket thinking it was an air leak. The owner called a buddy of his from San diego who came up during the weekend to look at my shee and after about an hour of fucking with it the guy was playing with my slide and noticed the needle was bent just a little. they put it in the carb and slid it up and doen and it was hittind inside the carb. They put the engine back together with all new gaskets, plugs,crossover tube and with a new needle and the bit ran perfectly...They dialed in the jettign for me and I paid just for the diagnostic to see what was wrong and the needle I think I paid like $100 for 3 weeks in the shop, engine tear down,a new needle, and some extra stuff that I bought.
Clean the cabs real good and check your jetting and needle.