make sure your carb boots are connected properly, also have you done any engine modifications that might throw off jetting. also check stator voltage and make sure its putting the correct amount of volts out. remember eingines need air fuel and spark to run. the problem probably lies in one of the three.
does your reverse light flicker while riding? Check to make sure the reverse switch connection ( below the sprocket, left case side) is tight and clean. Also make sure that the parking brake switch/connections are clean and tight.
Either of these, when malfunctioning, can make the CDI invoke the RPM limiter, with the ensuing coughing/sputtering.