He will need a 1999 3.0l manual trans computer, 2WD or 4x4 won't matter, also flex fuel or non-flex fuel to match what he has now.
1999 was Rangers first year of PATS
When you change the computer you also have to deal with PATS(passive anti-theft system)
1999 has Type B PATS, so has a PATS module in the dash behind passenger side air bag.
This module is "married" to the one computer, only Ford can "re-marry" these parts, so to swap computers you need to get the PATS module that came with the new computer, and swap out both.
And then you also need the PATS keys that came with new computer, how ever a Mobile Locksmith can add your current keys to new PATS module/computer, not sure on cost???
Some say you can "tape" a working PATS key, that came with new computer, to the steering column next to PATS antenna, and that works, never tried it myself.
You might make some inquiries to Ford computer tuners to see if they can change computer software to Manual trans, would be easier, but not sure about cheaper.
So you keep existing computer, no PATS issues.
All Rangers have the base wiring for manual or auto trans, the difference is the trans wiring harness that plugs into the main/base harness.
He will need a Clutch safety switch and it's wiring, it plugs into existing wiring after NSS bypass is removed.
NSS(neutral safety switch) on an auto also has Reverse Light wiring, you can splice manual tran reverse switch into that or get the whole harness, but I think splice would be easier.
You need a 5-speed that has bell housing for 3.0l engine, trans from anything else won't work, it also needs to be from a 4x4, 2WD trans won't work.
Then the clutch/brake pedal assembly
And steering column change over
Overall it is not an easy change over, IMO, unless you have a rolled or otherwise damaged 1999 3.0l 4x4 manual trans truck to get all the parts from, you would be better off selling the auto trans truck and buying a manual trans truck