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The aftermarket exhaust is probably not throwing off the mixture much, as I run mine straight pipe and never had to re-jet from stock and it runs great, but the air filter setup will. If you do not have the stock airbox then your constant velocity carburetor will not have the same vacuum and will not have the same fuel/air mixture.
One last educated guess would be a vacuum leak. I had a dirt bike that did the exact same thing for years and I lived with it, only to discover the problem was a cracked intake boot. I sprayed water all over my engine and noticed the idle sort of stumbling. Then I narrowed it down with a squirt bottle. Other that bad fuel air mixture or vacuum leak I'm not sure what else it could be.
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