A mismatch between the injectors and aftermarket MAF will cause problems. Put the stock MAF on the car and some of your problems will clear up.
Here's some additional information on MAF's
The MAF body and sensor are designed to match each other. Type A sensor works with Type A bodies. The bodies and sensors are not necessarily calibrated together to create a precision matched pair. You can't swap sensors between different part number MAF bodies and maintain proper calibration.
The output voltage of the MAF is a function of the air flowing through it. The MAF itself does not know about injector sizes, nor does it care. All it sees is that an increase in airflow means a corresponding increase of MAF output voltage. Altering the design of the MAF body can alter the flow past the sensor.
The OEM ford system was designed to use internal computer tables to match the voltage output of the MAF to a calculated injector turn on time. The injector table uses only one size injector in its calculations. This is a much more accurate means of determining the engine’s fuel requirements. Using a different MAF than the one the computer was designed for can upset the computer's calculations and the air/fuel ratio.
What aftermarket MAF’s do is try to fool the computer by either changing the amount of airflow over the stock electronics (C&L method) or by altering the sensor itself (Mass Air Systems method). The goal for both methods is to change the output voltage of the MAF so the computer calculates new data that is used to vary the pulse width sent to the injectors.
The only other MAF that is a one for one swap for a 93 and earlier 5.0 Mustang is the 94-95 Mustang MAF.
94-95 Mustang GT MAF - $40-$100. It is 70 MM instead of the stock 55 MM on regular stangs built prior to 94. It uses a slip on duct on the side that goes to the throttle body and a 4 bolt flange on the other. You need a flange adapter to fit the stock slip on air ducting that goes to the air box. Wiring plugs right in with no changes.
*2.) MAF & sensor interchange
The 94-95 Mustang 5.0 MAF & sensor is also found on:
1995-94 Mustang 3.8L F2VF-12B579-A2A,
1994-92 Crown Victoria 4.6L F2VF-12B579-A2A,
1995-94 Mustang, Mustang Cobra 5.0L F2VF-12B579-A2A,
1994-92 Town Car 4.6L F2VF-12B579-A2A,
1994-92 Grand Marquis 4.6L F2VF-12B579-A2A,
Evidently the –A1A, -A2A, AA, etc. on the end of the part number is a minor variant that did not change the operating specs. You should be able to ignore it and have everything work good.