this engine's got reed valve intake.. So, a piston ported intake 2-stroke's "normal" four-stroking and misfiring at low rpm is eliminated.
There's no missing at idle if it's set up right .. my bike idles steady at very low RPM... And no misfiring at higher RPMs either. The stock bike is about as smooth and quiet as a sewing machine if it's in perfect tune.
Since you already went through the carb/fuel system, i'd first suspect a vacuum leak, particularly where the carb meets the reed valve intake block.. That joint tends to leak. It did on mine. Gaskets dry out and shrink and crack..
Spray a bit of Starter Fluid around the area.. a change in rpm indicates a vacuum leak.
A coating of Permatex 2 (non-hardening gasket sealant) on the offending gasket / joint will cure it.. but there's no cure for this freakin design where you gotta drop the engine to get to it.
Or it may be reed trouble.. I've played with the reeds and they are very simple.. easy to diagnose.
Either the stainless steel petals lay perfectly flat against their seals or they don't. If they don't, the misfire-symptom could be the result (some fuel mix is regurgitted backwards into the carb causing a rich-misfire). I haven't seen cracked petals but it does happen.. A close inspection will reveal whatever may be wrong with them. If you remove the petal screws for any reason, be sure to use LocTite on them when reassembling.
Lastly (should be firstly) try a new spark plug..