Simple as this, you are running way to lean, the jetting and all is correct, BUT you have a new exhaust and new filter, The K&N with the lid on gets enough air as it is, but with the lid off you are getting to much air... TO MUCH AIR is the problem... dont go down on the main jet, try going up instead

 

i ride a 400ex with pretty much the same type of mods you have, pipe, nerfs bumper, ect.

where do you usually ride?

i cannot go this weekend, i already made plans to ride in grindstone.


PS: i live in perryopolis, and go to frazier