Adding to what DirtDonk wrote...
Back in the day, no one knew how to use the distributorless ignition system on an Exploder 5.0, so they removed it (including me, until I got help from an EFI Master back in 2005). Those days are past. Since you are new to this, remove as much of the under hood wiring back into the cabin as possible, carefully, intact. You won't need most of it. But better to have it and not need it than the other way around.
904Bronco is an ace at these swaps, has done several. He keeps all the OEM emissions stuff, but you don't have to (though I would read anything he has posted about his swaps carefully, he is good at this).
Mechanically, the engine is a direct bolt-in. Uses stock Bronco motor mounts, among other things. A few bits to connect the Explorer power steering pump to your existing box. The Explorer alternator puts out a lot more juice than the Bronco unit, so some wiring needs upgrading to avoid melting things.
No need to change radiators, my ancient OEM-spec 3 row Modine radiator cooled my basically stock Explorer 5.0 for 20 years and 120,000 miles of driving in all sorts of conditions without issue. It would probably have cooled my new 408 except that it chose the moment of the recent swap to die, a topic for another thread.
Use the Explorer transmission, you need an adapter to the transfer case and may need to move it back (I know nothing about this, I'm a manual transmission guy with an NV400 + Atlas and Advance Adapters crossmember).
Fuel system is all electric, no more mechanical pump, so you need an in tank or external pump, a source of never-ending debates. The plumbing is more complicated than stock, either way.
You can keep the 90° elbow on the intake or remove it and bolt the throttle body straight to the upper intake. Your choice.
Keep the OEM exhaust manifolds or use headers, your choice. I made things hard on myself because I wanted headers and 22 years ago there were no options that fit GT-40P heads. That has changed.
You'll eventually want to simplify the engine harness to get rid of all the irrelevant stuff, though not before you have educated yourself. I understand that EFIGuy has videos on how to do that. He can also reprogram the engine control computer to turn off things you don't need, like the passive anti theft system.
It may seem intimidating at first, but don't overthink it. Most stuff just bolts in. And once you are done, it just runs. And runs. And runs.
So here is the flip side of the coin. Please don't construe anything that I post as my preference, my belief, or my prejudice. It's just that the internet is something of an echo chamber...and if you don't have both sides of the arguement...then it really isn't an arguement.
Yes, obviously you can jack up the radiator cap, and park an Explorer under it. So yes...as long as you use all of crap that came with the Explorer, you can convince yourself that it is a good swap. But there's that pesky "Check Engine Light." When you start removing things that are deemed "unnecessary" then the CEL comes on. So in order to make the thing run...you MUST have a custom ECU. (Don't pretend that just because you flash your old ECU with a new program that you didn't invent a new ECU. That's just silly semantics. If I can't go to Autozone and buy an ECU to drop in...then I need a "custom" ECU.)
Which gets us to the crux of the issue. What "Custom" parts do you want to use? Is there aftermarket support? What is the common failure mode, or MTBF for the custom parts that you employ? Can you take it to a shop and have it serviced? Can you take it to a Dealer and have it serviced? Who knows how to fix what?
All of these Explorer swaps rely on ONE GUY who has the magic recipe to make your computer function. (it turns out that there is more than one "one guy" but if you don't know who the "other guy" is...then it's really only ONE GUY. Every time the EFI GUY cuts a fart, or doesn't answer his phone...the forum goes crazy because they can't get their Explorer to run. The beauty of the 89-93 Mustang 5.0 EEC-4 system is that it doesn't use any custom computers. The ONLY custom part on the 89-93 Mustang system is the wiring harness. And the MTBF on a wiring harness is somewhere greater than my lifetime. Ron Francis / The Detail Zone / RJM have invented a new harness with 4 relays in it. But those are COTS parts from TE. (Commercial, Off the Shelf). So yes, there are 2 more components that can fail...but the factory used 2 relays (EEC power, and Fuel Pump), so you are only adding two relays that are readily available. The EEC is the famous A9L, or A9P and there were hundreds of thousands produced, and the 60 pin EEC4 format is supported in the aftermarket. Granted, they are 30+ years old...but you can still buy them, and they are still serviced.
The aftermarket has adopted the 89-93 Mustang 5.0 as the swap of choice in Early Mustangs, and Cobra Kit cars. Also in 79-88 Fox upgrades. So that platform has reached critical mass, and you can get service nationwide. And the Internet is full of support. The diagnostic port works with all EEC-4 code readers, and the check engine light functions.
So that leaves us with the Explorer 5.0 benefits vs the 89-93 Mustang benefits. So lets look at the major differences:
1. Engine management.
2. Transmission management.
3. Oil Pan.
4. Cylinder head exhaust ports.
5. Induction.
6. Valve covers.
7. Ignition
8. EGR / Thermactor / EVAP / Downstream O2 / catalytic converter (how many sensors do you really need?)
If you are NOT going to run a Catalytic Converter, then the multiple O2 sensors are useless. If you are not going to run EGR, EVAP, or Thermactor, then those can also be deleted. So what's left? It's not just coil packs vs. distributor. That discussion has been resolved. Coil packs provide ZERO additional benefit over a properly functioning distributor. The ONLY advantage to a coil pack is that you can have the waste spark enabled...and that doesn't make it run better. Consider the 97-02 Jeep Wrangler 4.0 versus the 03-06 Jeep Wrangler 4.0. The only difference between 02 and 03 is coil packs. After 20 years, and millions of data points...no one can point to an improvement with coil packs. (PLEASE don't argue that waste spark is "better" when you have deleted all of the other emissions equipment...)
Now, if you need transmission management, that opens the door to the Explorer ECU a little...because you get built in transmission control. The aftermarket AODE/4R70 controllers are very reliable, but I can see wanting that function integrated into the factory ECU. But everybody knows I hate automatics, and so it's not something I think about much. If I'm going to run a 4R70, I would modulate it with a throttle valve, and that's a whole different can of worms. But yeah...AOD with 4R70 gears, and then I'd still have an automatic. So no.
(and just to prove that this is not a total rant...I am putting a 6R80 behind my Gen 1 Coyote using a PBH control pack. And yes, I am aware that the 6R80 is an automatic transmission.)
So now we are left with p-heads. Since I run factory cast iron manifolds...its a no-brainer. Avoid p-heads.
So we are left with 89-93 Mustang engine management on a 96-97 Explorer 5.0. DONE.
All of this is driven by my recent interaction with Holley regarding their ProJection 2DI product support. How long should an obsolete product be supported? The answer to that question is hugely philosophical. Think of MS DOS. or Windows Embedded. Or iPhone 3 jailbreak. Or Ford 9 inch ring and pinion. Or Cessna 172 door handle. (when was the first 172 airframe certified?)
Gotta go.