Could be, were these replaced during the rebuild? - sorry just re read your initial post where you stated you had.
It would be the very last thing i would check though.. for the obvious reason that its frickin expensive and annoying stripping it down again.
2 strokes only ever go wrong in 2 ways - BIG TIME or something really simple yet annoying haha
Other thing is...crms are fickle little buggers sometime. My last mk3 was rebuilt with top bits, but did something similar to what you describe. Could never stop it as it seemed to just be what the engine wanted to do. I turned the idle screw right out so it was just pop... pop..... pop...but wouldnt idle when cold without the choke (not left that on have you! Mine used to rev its tits off if the choke was left on more than 30 seconds)
once warm though it would just sit there ticking over lovely.
As a starter though, put all the jetting back to standard (unless you have a full dep on it). Make sure the air filter is oiled (otherwise itll run lean)
Take it out for a spin and do a plug chop. Thats the simplest way of seeing how its running.
Paul