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I haven't messed with the air filter, so it is stock. I probably need to change it, but I don't think it is so dirty it is causing it to run that way. Maybe it is timing then?
Did you run a full exhaust or just a slip on? Cuz with a full exhaust you will need to rejet and use an aftermarket filter. If it's just a slip on, you shouldn't have to rejet at all or change your filter from oem.