Dave on this forum has a build thread on his swap. Do a search. He did an excellent job describing his installation of a complete, intact Explorer 5.0, including the PATS anti-theft system, all cats, custom fuel tank utilizing the Explorer pump, vapor recovery system, etc. He also used the 4R70W automatic so the PCM is controlling everything as Ford intended.
I'm running a bastard combo. It's an EEC-IV system using an A9L PCM, with a Tweecer to turn on the EDIS functionality (the A9xx PCM's had EDIS capability built in to the software, but Ford never utilized it in a production car), and an EEC-IV EDIS module from a 1994 Crown Vic (starting in 1992 the Crown Vic got the 4.6 liter mod motor; the PCM didn't have built-in EDIS control capability, but instead depended on an external module, essentially replacing the TFI module found on the Windsor engines). I created the engine harness from parts of a Mustang 5.0 harness, Explorer 5.0 harness and the Crown Vic donor. It looks cool, gives me some bragging rights and theoretically has more stable timing (now controlled off the crank trigger instead of the distributor) but really it doesn't run any better than it did with the TFI distributor. Plus, getting it to run right required learning the Tweecer and related software. Not for the faint of heart.
Since I have a manual transmission and will probably move the whole mess to a 351W stroker eventually anyway, the factory Explorer hardware doesn't interest me too much- and besides, I like to experiment. But since you have the intact Explorer 5.0 and related hardware, I would tend to agree with the others that recommend the complete Explorer install. Ford learned a few things over the years; I've never driven a 5.0 Explorer but I'm guessing that keeping the EEC-V system intact would make for a very nice-running package.