If you have the wiring harness for the 1996 5.0l and PCM(EEC-V 104-wire) then use it, it will work fine with a manual trans, and you can, at some point in the future, have the PCM's auto trans software deleted, that would turn off the CEL
Local Speed Shops or Dyno test shops will know Locals who can delete that software, also do tunes you may want to add, usually the minimum charge is $200, or was, lol
The 5.0l(302) in other Ford models was discontinued with the older EEC-IV 60-wire PCM in 1995
So older PCM would need the older wiring harness
Explorer/Mountaineer 5.0l was the only EEC-V after 1995, and ALL V8 Explorer/Mountaineer were automatics
There are many older 5.0l manual trans PCMs, the A9L was the most popular, but you need the wiring harness
As a reference
EEC-IV PCM 60-wire was OBD1
EEC-V PCM 104-wire is OBD2, still used today
EEC-IV use external spark system, so you had a separate spark "module" and the PCM
EEC-V had spark system in the PCM, all-in-one
So the wiring harness's were quite different, not just the number of wires