I'm not sure about pre 2004, but if you try to install an '04 or later modular engine in a non-standard vehicle you have a few challenges in your future. The stock computer is networked with several modules throughout the vehicle. The ABS computer, gauge cluster, PATS anti-theft module, just to name a few. For example, if I disconnect my ABS sensors the bronco will run just great, right up to 41 mph. When you get to 42 it triggers a P2106 DTC and decides to run like crap until you restart the engine. If you get both front sensors working but forget the back you'll go as fast as you want, but the DTC will hit you randomly instead. This is great fun on a road trip, especially if you have your wife along. If you don't include the steering column or at least the antenna built into it, the thing won't even turn over because it needs to get a signal from a key programmed for that computer. Forget about hot-wiring it. All the spark plug wires and injector wires come straight out of the ECU. The gauge cluster also uses a vehicle speed signal which it converts and sends to the other modules for things like cruise control and I can't remember what else. I almost forgot the transmission! The transmission is covered with sensors that the computer uses to coordinate with the electronic throttle to maximize shift quality. Unplug one of those things and you're getting codes like crazy. This means you're not going to use a non-standard transmission very easily. You might get away with it if you used the guts from a 5.4L with a manual trans, but I suspect you'd need to replicate some speed signals somehow. The VSS input also no longer comes from the rear axle. It gets computed from the output shaft speed of your transmission through a little sensor mounted in the casting. There's still a sensor on the axle, but it's only used for ABS.
I'm not trying to discourage anyone, just lay out what you've got ahead of you assuming you can make everything fit dimensionally. Even in my full size bronco I still had to notch the frame to make the 5.4L fit. If you really want to put a new modular engine in your rig (again I can't speak for pre-2004) I'd look for an aftermarket computer that's made specifically for it (if one exists). That way you wouldn't need all these modules I listed above. I had one guy tell me he thought a tweecer could do the same thing, but I haven't even explored verifying that. My impression is a tweecer can modify settings, not tell your ECU to disregard an integral part of its programming.
Lovin' those positive comments about my project.