The wiring that's there is pretty useless without a 5.0/AOD to plug it into, you'd definitely need the 4.6 stuff if you don't want a major wiring project since there are so many extra circuits.
Ideally you should get the EEC/CCRM harness, engine harness, transmission harness and PCM out of a 96-97(94/5 would work but needs even more modifications with the PI motor), and splice in connectors to make them mate up with the stock main underhood harness and dash harness properly.
EDIT: You'd also need to run the transmission wiring circuits from the EEC harness through the dash since the AOD isn't electronic, 94-97 dashes have that wiring integral. There are several circuits that need to be run from various places and may be more work than most would be willing to tackle. If you do a 94+ dash swap simultaneously(I recommend 94/5 since the firewall connector is the same size and basic pinout as 89-93) this would be easier.
I have to agree with others, find a 5.0 to put back in it, it really is a lot simpler. Find the
GT40 heads and intake out of a 96 Explorer and it'll basically be the equivelant to a 4.6 PI