The stock ECU has the ability to change the mixture roughly +/-20% and retain that change in memory. But it takes time to stabilize, in my experience, and the engine needs to be runs under varying conditions. It seems unlikely to me that an air cleaner alone could cause the mixture to be off greater than 20%.
Note that adjustment is lost if the battery is disconnected, which is one of the huge advantages of an unlocked ECU. With an unlocked unit you can run the car under various loads and allow it to self adjust, then using the ProTune software you can permanently save the new map. If more adjustment is required run the car again, and save the newly adjusted map again. After I changed my exhaust (de-cated and free flowing mufflers) and air cleaner I did three iterations of this process and it made a significant difference.
