If you got any crap down into the combustion chamber it may be burning off. When i cleaned mine it ran rough at first but cleared up after a few minutes. Are sure everything is tight? Did you use new gaskets?
06 GMC Sierra 2500HD Dmax/ally
06 Pontiac G6 GT
05 CRF250R
FOR SALE 06 KX65 with riding gear $2700 obo