Next, do a complete engine tune and service, following the instructions in the manual, to eliminate any other potential problems.
Still not running right, next step would be looking through the carb, because it's cheaper than electrical problems. Completely disassemble the carb, then carefully clean and inspect each piece for damage or wear. Replace worn and damaged parts. Reassemble carb making double-dawg sure every piece in the parts explosion is used. Adjust float height as directed. This is critical. Install the #118 jet. Visit a hardware or hobby store for a single flat washer to slide up the needle shaft to raise the needle. Set the pilot screw about 2.5 turns out. If the carb had problems, and you did the carb work properly, these settings will be so close to perfect you probably will not want to ever touch them again, unless you ride way up in the mountains or something.