The stock heads are the bottleneck - they limit the flow so badly that any change in throttle body size is a waste of time and money.
See
https://www.stangnet.com/mustang-forums/threads/flow-rate-for-5-0-cylinder-heads.713161/post-7027297 for the flow numbers.
OR
Head Flow Data In CFM-Source:
http://users.erols.com/srweiss/tablehdc.htm#Ford
Head......................................Head CC..........Valve sizing (Int/Exh)...Flow at .500” lift
E7 Irons............................................. ......................1.78/1.45........... 159/109
If you put high flow cylinder heads on, you will need to update the Speed Density computer system to Mass Air computer.
Computer system differences in 86-95 Mustangs.
Revised 15-Jan-2018 to add requirements for larger fuel system components to support large changes in airflow through the engine.
All 5.0 foxbody engines from 86-95 are OBDi
OBD1 comes in Speed Density and Mass Air Flow versions. It differs from OBDII in that diagnostic data cannot be streamed through the diagnostic port in a real time mode. The diagnostic data is stored in volatile memory and dumped on command by an external jumper or code reader connected to the computer’s diagnostic port. Watching the Check Engine Light, an external test light or voltmeter are all that is need to dump the codes on an OBDI system. An OBDI code reader can be used, but it isn’t an absolute necessity.
ODBII is capable of streaming data through the diagnostic port in real time mode. It requires a code reader that handles the OBDII data format. No code reader, no way of knowing what the codes are. The plus is you can watch changes in sensor data as they happen, and use the information to plan changes in the computer's program. OBDI requires a laptop & some specialized hardware to do the same thing.
Both OBDI & OBDII have adaptive learning to accommodate changes in sensor output, so as the sensors and airflow values change, the computer adjusts for them. Mass Air systems have a greater range of adaptive learning than Speed Density.
Speed Density uses Manifold vacuum (MAP), Throttle position (TPS) and RPM, & Air Temperature (ACT) to guess how much air the engine is pulling in. Then it uses all of them plus the O2 and ECT sensors to calculate the air/fuel mixture. It is dependent on steady manifold vacuum and minimal changes in airflow from the stock engine configuration to maintain the proper air/fuel ratio. Change the airflow or vacuum too much and the computer can't compensate for the changes, and does not run well. Forget about putting a supercharger, turbocharger or monster stroker crank in a Speed Density engine, because the stock computer tune won’t handle it. Every time you seriously change the airflow through the engine, you need a new custom burned chip to make the engine run at peak performance. Most aftermarket cams will not work well with Speed Density, and that includes the Ford letter cams.
Mass Air uses a Mass Air Flow meter (MAF) to actually measure how much air is being pulled into the engine. The computer uses this information and inputs from the O2, TPS, ACT, ECT, RPM and Barometric Pressure (Baro) sensors to calculate the proper air/fuel ratio. It is very tolerant of changes in airflow and vacuum and tolerates wild cams, high flowing heads, and changes in displacement with minimal difficulties. Just remember that large changes in airflow require more fuel than the stock fuel system can deliver. At that point, you will need larger injectors and a larger fuel pump to make the engine run like it is supposed to. Larger injectors can be used with either an aftermarket calibrated MAF or a custom dyno tune. This makes it possible to use the stock computer with engine displacements from 302-408 cu in, and make many modifications without a custom dyno tune chip. Put a new intake manifold on your 331 stroker and the computer figures out how much more fuel to deliver without having to have a new chip burned to accommodate the extra airflow.