You likely have an air leak or a vacuum leak. Inspect hoses and ducts carefully. Starting with your air filter housing. Make sure the two halves are locked together all the way around (NOTE: this is very difficult with a K&N air filter unless you take the housing out and assemble it on a bench). Any gap between the two halves will result in rough running, and Check engine Lamp. Also check the rubber grommet where the MAF sensor wiring comes out of the air filter housing. Make sure it is seated fully. If you have any rubber elbows or couplings in your PCV tube, make sure they are not deteriorated and loose.
