Did you replace the coils when you rebuilt the engine? Sounds like one coil is firing erratically (going bad) causing the carbon build up.
Try disconnecting the plug wire on the right side to see if the engine runs with the opposite cylinder connected. Then, pull the wire on the left side leaving the other plug wire connected. The side that runs rough or not at all is likely the problem due to a bad coil. Sometimes the engine will backfire if the coil is bad due to carbon build up (not good for the muffler).
My CH 18 did the same thing. Going to tackle the problem in the fall as I have other projects in the pipeline.
Good luck with your CH20!
