TTR 250 engine missing a beat

Hi
Not long ago i bought a 1991 TTR 250 and it doesnt work!!! at first there was a major flat spot when taking off, which i thought was going to be a carby issue, but it turned out to be the inlet manifolds, which have now been replaced. but now the engine misses a beat! it can usually idle fine but when riding it will cough and splutter and jolt, and then carry on (the movement seems to keep it running), but when it gets hot it misses when idling and dies completely. the carby has been cleaned twice now so im fairly sure its nothing to do with that.
has anyone had similar problems? is it easily fixed? any help would be much appreciated

James

Remember a 68 Chevy Impala (loved the car), I had that exhibited some of the same things. As I jumped into it, thought carb, then intake, then timing. I had replaced the chain and crank gear. Then while adjusting the valve train, I noticed a rocker not moving at all. Turns out the cam had a lobe that was flat. Replaced cam and all was well... Hope this helps somewhat...