Thanks Rob!
Already replaced the air filter (Which was filthy) with a new K&N. Helped a bit, but not tremendously.
The shudder is isn't so much a slow start or hesitation but happens under load. It feels the same as if a fuel filter was partially clogged in a petrol engine, just a momentary loss of power. I notice this around 3500 rpm. I assumed it was too much fuel being dumped since this and the black smoke seem to happen at the same time- assumed the power loss was from un-ignited fuel?
Next thing I'm going to check is the Altitude compensation system, if it's there, will also give the 2 stroke a shot.