I kind of thought that was the case. Being that I have no idea of how you wired the electric fuel pump circuit, here's both sets of diagrams.
My best guesst is that since this was a mass air conversion type operation that the 86-90 code 96 and diagrams are the best choice. There is an extra wire that gets run that may not be part of the conversion harness.Connect it up or add it in and the 96 code goes away in most cases. It ran from the pink/black wire on the fuel pump relay to pin 19 on the computer.
The following is a view from the computer side of the computer wiring connector: it is for an A9L, A9P computer.
Code 96 for 86-90 model 5.0 Mustang – KOEO- Fuel pump monitor circuit shows no power - Fuel pump relay or battery power feed was open - Power / Fuel Pump Circuits. The fuel pump lost power at some time while the ignition switch was in the run position. The main power feed to the pump is what is losing power.
Look for a failing fuel pump relay, bad connections or broken wiring. The fuel pump relay is located 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
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 the test connector is 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.
86-90 Models:
Using the diagram, check the red/black wire from the fuel pump relay: you should see 12 volts or so. If not, check the inertia switch: on a hatch it is on the drivers side by the taillight. Look for a black rubber plug that pops out: if you don't find it, then loosen up the plastic trim. Check for voltage on both sides of the switch. If there is voltage on both sides, then check the Pink/black wire on the fuel pump relay: it is the power feed to the fuel pump. Good voltage there, then the fuel pump body to tank wiring harness connector is the likely culprit since it is getting power. No voltage there, check the Orange/Lt blue wire, it is the power feed to the fuel pump relay & has a fuse link in it. Good voltage there & at the Pink/black wire, swap the relay.
Keep in mind that the relay wiring and socket can also cause intermittent problems. Clean the relay socket with non-flammable brake parts cleaner or electrical contact cleaner. If you find damaged wiring at the relay socket, replacement pigtail socket assemblies are available at the auto parts stores. Be sure to solder the wires and cover the solder joints with heat shrink tubing if you replace the relay socket.
Code 96 causes & tests 91-93 models. – KOEO- Fuel pump monitor circuit shows no power - Fuel pump relay or battery power feed was open - Power / Fuel Pump Circuits. The fuel pump circuit lost power at one time or another.
Revised 07-apr-2013 to add check for corrosion and damage in fuel pump relay socket
Clear the codes by disconnecting the battery and turning on the headlights for about 5 minutes before reconnecting the battery. This will clear any remaining codes. Drive the car for several days and dump the codes again. In many cases, this clears the 96 code.
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
Mustang Mass Air Conversion | StangNet
Diagram of the fuel pump wiring for 91-93 cars.
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 the test connector is 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. No voltage when jumpered, check the fuel pump relay and fuse links.
Power feed: Look for 12 volts at the pink/black wire (power source for fuel pump relay). No voltage or low voltage, bad fuse link, bad wiring, or connections. Remember that on 92 or later models the fuel pump relay is located under the Mass Air meter. Watch out for the WOT A/C control relay on these cars, as it is located in the same place and can easily be mistaken for the fuel pump relay.
Relay: Turn on the key and jumper the ECC test connector as previously described. Look for 12 volts at the dark green\yellow wire (relay controlled power for the fuel pump). No voltage there means that the relay has failed, or there is a broken wire in the relay control circuit.
Be sure to closely check the condition of the relay, wiring & socket for corrosion and damage.
91-93 Models:
Using the diagram, check the dark green/yellow wire from the fuel pump relay: you should see 12 volts or so. If not the relay has failed or is intermittent. Check the inertia switch: on a hatch it is on the drivers side by the taillight. Look for a black rubber plug that pops out: if you don't find it, then loosen up the plastic trim. Check for voltage on both sides of the switch. If there is voltage on both sides, then check the Pink/black wire on the fuel pump relay: it is the power feed to the fuel pump. Good voltage there, then the fuel pump is the likely culprit since it is getting power. No voltage there, check the Pink/black wire, it is the power feed to the fuel pump relay & has a fuse link in it. Good voltage there & at the dark green/yellow wire, swap the relay.
All testing is done with the ignition switch in the Run position. Do not forget this crucial step.
The pink/black wire s should have the same voltage as the battery positive terminal +/- 0.25 volt. If not, then the fuse link for the fuel pump has opened up.
With the test jumper in place the green/yellow wire should be the same voltage as the pink/black wire +/- 0.25 volt.
If not, look at the red wire: should have the same voltage as the battery positive terminal +/- 0.25 volt.
If not, then check the yellow wire on the EEC relay located on top of the computer. This one is hard to get to. It should have the same voltage as the battery positive terminal +/- 0.25 volt. If not, then the fuse link for the computer has opened up.
If the red wire does not have the same voltage as the battery positive terminal +/- 0.25 volt and the yellow wire on the EEC relay does, then check the red/green wire on the EEC relay. It should have the same voltage as the battery positive terminal +/- 0.25 volt. If not, then the ignition switch is defective or the fuse link in the ignition wiring harness has opened up, or the EEC relay is defective.
All testing is done with the ignition switch in the Run position. Do not forget this crucial step.
The pink/black wire s should have the same voltage as the battery positive terminal +/- 0.25 volt. If not, then the fuse link for the fuel pump has opened up.
With the test jumper in place the green/yellow wire should be the same voltage as the pink/black wire +/- 0.25 volt.
If not, look at the red wire: should have the same voltage as the battery positive terminal +/- 0.25 volt.
If not, then check the yellow wire on the EEC relay located on top of the computer. This one is hard to get to. It should have the same voltage as the battery positive terminal +/- 0.25 volt. If not, then the fuse link for the computer has opened up.
If the red wire does not have the same voltage as the battery positive terminal +/- 0.25 volt and the yellow wire on the EEC relay does, then check the red/green wire on the EEC relay. It should have the same voltage as the battery positive terminal +/- 0.25 volt. If not, then the ignition switch is defective or the fuse link in the ignition wiring harness has opened up, or the EEC relay is defective.
Diagram courtesy of Tmoss & Stang&2birds