If I recall correctly, this vintage of Mustang is MAF equipped (mass air flow). Air filters simply do not catch 100% = I'll bet you that the MAF sensor is dirty, which will cause drivability issues without necessarily setting codes (even highly experienced ASE Master Techs / Advanced Drivability Specialists miss this one). There should be two anti-tamper Torx screws holding the actual sensor (black plastic rectangular item) down to the MAF assembly casting. Remove the actual sensor and look for a tiny hotwire spot welded to 2 thicker pegs. Any dust, dirt, fuzz (and I mean magnifying glass visible) on the actual hot wire will insulate it from reading the appropriate amount of actual airflow entering the engine. The PCM adds fuel based upon the amount of air entering into the engine, and will skew the fuel tables to the lean side if it is reading low amounts of air to the PCM. Having said all of this, I advise you respect how delicate this sensor is. One wrong move and you will wreck it and they are not cheap to replace. This is also applicable to most all hotwire type MAF cars (there is also a siphon type design that is less sensitive to dirt) - you would be suprised how much better a vehicle can run when the MAF sensor is cleaned (providing it was dirty).
Hey wait a second, aren't you the hydroboost guy?? LOL 