The proper computer to use is either a Ranger or Explorer manual trans computer for either 1991 or 1992 (there were SEVEN 1990 M/T 4.0 trucks built)
the 1993 computer is slightly different and would cause "issues"
and a 1994 would not work at all.
The main difference with the M/T computer is the way it manages the engine on idle
and over-run (engine braking)
With a manual trans computer about 1.5 seconds after the throttle is closed
and the engine rpm is above 1400rpm the computer will cut ALL the injector pulses
until idle falls to or below ~1000rpm.
This reduces waste of fuel and improves the effectiveness of "engine braking"
An auto trans computer keeps the front pump in the trans working, because if that pump falls below it's stall speed (different from the stall speed of a torque converter) it allows the converter clutch to release.
in any event the engine will run with a manual trans and an auto computer, but it will typically set error codes for the Torque converter lockup solenoid and the 3-4 shift solenoid (which are obviously not connected)
having a manual trans computer will improve driveability and in my experience can net you 1.0-1.5mpg if you live in hilly country.