Engine codes 41, 91, 66, and 96?

Your codes of 41, 91, and 96 are all a result of what you've removed/disabled from the car. Regarding the 66, what brand of maf are you running?

Code 41 or 91 - O2 indicates system lean. Look for a vacuum leak or failing O2 sensor.
The computer sees a lean mixture signal coming from the O2 sensors and tries to compensate by adding more fuel.

Measuring the O2 sensor voltage at the computer will give you a good idea of how well they are working. The computer pins are 29 (LH O2 with a dark green/pink wire) and 43 (RH O2 with a dark blue/pink wire). Use the ground next to the computer to ground the voltmeter.
The O2 sensor ground is in the wiring harness for the fuel injection wiring. I grounded mine to one of the intake manifold bolts

"When the mixture is lean, the exhaust gas has oxygen, about the same amount as the ambient air. So the sensor will generate less than .4 volt. Remember lean = less voltage.

" When the mixture is rich, there's less oxygen in the exhaust than in the ambient air , so voltage is generated between the two sides of the tip. The voltage is greater than .6 volt. Remember rich = more voltage.

Here's a tip: the newer the sensor, the more the voltage changes, swinging from as low as 0.1 volt to as much as 0.9 volt. As an oxygen sensor ages, the voltage changes get smaller and slower - the voltage change lags behind the change in exhaust gas oxygen.

Because the oxygen sensor generates its own voltage, never apply voltage and never measure resistance of the sensor circuit. To measure voltage signals, use an analog voltmeter with a high input impedance, at least 10 megohms. Remember, a digital voltmeter will average a changing voltage."
Charles O. Probst, Ford fuel Injection & Electronic Engine control

Code 96 – KOEO- Fuel pump monitor circuit shows no power - Fuel pump relay or battery power feed was open - Power / Fuel Pump Circuits. At some point in time, the fuel pump lost electrical power while the engine was running.

Look for a failing fuel pump relay, bad connections or broken wiring. The fuel pump relay is located under the Mass Air Meter on Fox bodied stangs built after 91. On earlier model cars is under the passenger seat. On Mass Air Conversions, the signal lead that tells the computer that the fuel pump has power may not have been wired correctly. See http://www.stangnet.com/tech/maf/massairconversion.html

To help troubleshoot the 96 code , follow this link for a wiring diagram http://http://www.autozone.com/images/cds/gif/large/0900823d80195960.gif

Look for power at the fuel pump - the fuel pump has a connector at the rear of the car with a pink/black wire and a black wire that goes to the fuel pump. The pink/black wire should be hot when jumpered to the test position. . To trick the fuel pump into running, find the ECC test connector and jump the connector in the lower RH corner to ground. http://www.mustangworks.com/articles/electronics/eec-iv_codes.html for a description of the test connector. it. No voltage when jumpered, check the fuel pump relay and fuse links.

Code 66 MAF below minimum test voltage.
Insufficient or no voltage from MAF. Dirty MAF element, bad MAF, bad MAF wiring, missing power to MAF. Check for missing +12 volts on this circuit. Check the two links for a wiring diagram to help you find the red wire for computer power relay switched +12 volts. Check for 12 volts between the red and black wires on the MAF (usually pins A & B).

The MAF element is secured by 2 screws & has 1 wiring connector. To clean the element, remove it from the MAF housing and spray it down with electronic parts cleaner or non-inflammable brake parts cleaner (same stuff in a bigger can and cheaper too).

There are three parts in a MAF: the heater, the sensor element and the amplifier. The heater heats the MAF sensor element casing the resistance to increase. The amplifier buffers the MAF output signal and has a resistor that is laser trimmed to provide an output range compatible with the computer's load tables.

The MAF output varies with RPM which causes the airflow to increase or decease. The increase of air across the MAF sensor element causes it to cool, allowing more voltage to pass and telling the computer to increase the fuel flow. A decrease in airflow causes the MAF sensor element to get warmer, decreasing the voltage and reducing the fuel flow. Measure the MAF output at pins C & D on the MAF connector (dark blue/orange and tan/light blue) or at pins 50 & 9 on the computer.

At idle = approximately .6 volt
20 MPH = approximately 1.10 volt
40 MPH = approximately 1.70 volt
60 MPH = approximately 2.10 volt

Check the resistance of the MAF signal wiring. Pin D on the MAF and pin 50 on the computer (dark blue/orange wire) should be less than 2 ohms. Pin C on the MAF and pin 9 on the computer (tan/light blue wire) should be less than 2 ohms.

There should be a minimum of 10K ohms between either pin C or D on the MAF and ground.

Remember that the computer does not source any power, but provides the ground necessary to complete the circuit. That means one side of the circuit will always be hot, and the other side will go to ground or below 1 volt as the computer switches on that circuit.

See the following website for some help http://www.autozone.com/images/cds/gif/large/0900823d80195960.gif