Fox body EFI was the go to choice from the late 90s until the Explorer swap was figured out. Yes it works.
Sounds like you are planning on putting the EEC-IV on the stock engine. Stuff you have in a box.
Do you know if it is mass air or speed density? Post the code off the computer and we will know. Mass air should be no problem. Speed density might be an issue as there is a difference in how well the old engine breathes vs what the computer is programmed for. Speed density doesn't know how much air is going in the engine like a mass air does. It has a programmed calculation where it looks at pressure, air temp, and RPM and from that it looks up how much air should be going through, sprinkles on the right amount of fuel, and at cruise will use the O2 to adjust to taste.
The other is the box of parts you are looking at will have a distributor for a roller cam. The bad thing is it will fit your engine. Bad as in the gear will be the wrong material and destroy stuff. Distributor gear will be the least of the worries. The cam gear will get destroyed, and in the process there will be iron shavings running around inside the engine. Late 80's crown vic has the right distributor for the EEC-IV and a flat tappet cam.