Yes, go 01 if its the best deal you can find.
With programming, you can shut off rear 02 sensors, and egr if required. I think this is what you are really asking.
If your willing to spend the cash and want to do it your self for learning and freedom of changes, you can go with an SCT programmer and a pro racer package. Also a member here that goes by decipha can make changes for you at root level programming if you wish. He appears to be extremely intelligent with this stuff.
You have lots of options on the programming side, no worries there.
That might be the member who I read of on the Corral who is most familiar with later Mustang PCM's, the 99-04 versions I believe. I'm hoping to find him again to help select my PCM's, for two of my four projects.
For a 2nd gen Explorer etc, skip the 95-97's, many deficiencies were corrected in 1998. The poorly designed torsion bar key pads make those poor choices. Buy a 98-01, the options/features are virtually the same, pick it based on the choice of fuel system and computer.
The 98 is the last return fuel system, 99+ are 62psi returnless. 98+ has PATS so swaps require a tune that disables PATS etc. As Don said, you can easily program out the EGR or rear O2, to keep the CEL off.
For performance, the stock PCM's will do what you want, better than the EECIV(they are just more advanced), but they will need some kind of better tune(at the end at the least).
The entire exhaust is crap, replace it all. Use two mufflers and two tail pipes, not one(that reduces flow by half), build some kind of manifolds(I'm doing log manifolds), and a pair of good 3" cats should work.
The truck automatics are poor choices for any "shift kits", becuase the truck VB calibrations often do not play nice with the VB kits. That's why some trucks have odd or poor shifting after the kits. Start with any comparable car trans, and the VB kits work as advertised.
BTW, the 2004 Mustang V6 has the last, best 4R70W in it. That one includes the "J Mod" already(it's factory engineer designed and Ford finally used it), and it has the SBF bell housing. Find those, it's the best for any automatic SBF vehicle to start with.
That PCM "expert" mentioned that he would prefer the Mustang OBDII computers, and that they could be utilized in place of the Explorer computer. Those will also control COP ignition, and best of all, it's faster and handles modifications much easier. But that will require modifications to the wiring harness, a tedious job. I'm going to do that with my new 98 Limited for sure, for the 14psi boost I'm aiming for.
So hunt the 98-01 Explorer/Mountaineer that you like the best, ignore mileage, go by the condition of the interior and other obsolete parts. The mechanicals and body are easy to keep up, the obsolete rubber and interior parts are hell to fix. I just bought this 98 Limited because it has all options without looking at the car, and it doesn't have the gaudy big wide fender flares. I have those on my 99, I still don't like them. The Mountaineers didn't get those thankfully.
The 2000 and 2001 Mountaineer had an optional painted grille. I don't really like the chrome one, so I've got a painted one that I'll like better I think.
For the computer, you can go with the old Fox stuff and its wiring, or the Explorer stock PCM/wiring, or alter the wiring some and go to the later SN95 PCM/wiring. All of them will take some programming. The EECIV has lots of knowledge out there. The Explorer is better but less people work with it, but everything revolves around a flasher(device that stores the programs(3-4)). Those take more time to swap.
The stock heads are poor, GT40 or P is low level flow. For power(300+), patiently hunt at least a TFS TW head, those unlock much more power above 5000rpm. Stock compression is 9:1 on every 5.0 ever made, for N/A get that to at least 10:1, it's worth it.
A 351W block bolts right in sure, but every external part is a PITA to modify to make it fit. It's been done a few times, and each person said they would never do it again. Nobody has done it twice(fab an oil pan, headers, distributor cam synch etc). Stick with the 302 block and set a decent price level. Do the exhaust and decide on the PCM, find the heads, build the 10:1 engine, swap it in, do the tuning. Have fun.