Did it used to run cleanly on top?
If it has always run that way, I would suspect that your main jet is too rich. Do you have a plug fouling problem? The stock KDX jetting is overly rich. Is it posible that you are still running stock jetting? Also, the stock airbox is pretty restrictive. You can remove the lid or put some holes in the lid and remove the snorkel. That could help fix your rich condition too.
If it used to run cleanly but won't any longer, I would suspect a rich condition caused by a clogged air filter or a clogged pipe/silencer. It could also be that your KIPS valve(s) is no longer operating properly.