Plug and cap are definitely suspect. With jetting I always like to get a base line of the motor to make sure I am not jetting to a unhealthy motor. Make sure you are getting a nice blue spark. Check reeds, compression and leak down. Make sure the pipe and silencer are clear of obstructions/heavy build up.
Removing the air box lid will allow for more air flow. I would recommend removing it if conditions allow. If you are running it mud or water, leave it on, otherwise invest in a prefilter. They do make pre filters that go in place of the air lid also.