You might have a leak in your intake seal. This happened to me after I had installed the aftermarket one, which “pulled” the throttle body closer to the front of the engine and damaged the rubber intake seal.
You can check live data in ProTunes for anomalies and also spray some starting fluid around intake seals to see whether it affects your idle.
The correct way to install a new filter would be: loosen intake manifold bolts, install new air cleaner (snug, but not all the way), tighten intake manifold bolts (snug), fully tighten Air cleaner bolts, fully tighten intake manifold bolts. (obviously you would need new seals if you do have a leak).
