Ryan,
You have to confirm that you are getting spark on both cylinders when it is running on only one.
You didn't switch out the CDI unit for one out of a Bonneville or Thruxton by chance. They are set up for 360 degree firing, not 270. Someone pulling a fast one on you???
Can you clarify when the engine runs on one cylinder? All the time, at idle, mid range or full throttle. Trying to see if the engine runs on two cylinders some of the time? Have you adjusted your idle mixture screws yet previously requested?
