Did it run fine before you rebuilt it? Was it a total rebuild or just the top end? Could be the pickup coil gap, I had the same problem, it was running on one side and i switched the plugs and the problem didnt switch sides. I even put on a new coil, cdi, harness, fresh piston rings, gaskets, alot more - I had about the same problem. Truned out to be something simple like my pickup coil gap being off. Its supose to be .018 go check that... Just my 2 cents. That problem costed me about 3 months lmao