Welcome to TRS
Manual transmission doesn't use, or need, computer control, automatics do.
1998 to 2000 Rangers used rear axle ABS sensor as the speed sensor for the speedometer/odometer so transmission wasn't involved, like earlier or later years
That means, with your 1999, you can use pretty much any year M5OD-R1 transmission from a 3.0l 2WD Ranger
3.0l Rangers all used the M5OD-R1 for manual transmission models, Mazda B3000 did as well
The M5OD-R1 transmission has integrated bell housing so is made for a specific engine.
The 3.0l Vulcan engine has unique bell housing bolt pattern, no match to any other engine.
2WD and 4WD transmissions, manual or auto, have different tail shafts so are not interchangeable.
You can disassemble your manual 2WD tailshaft and swap it to 4WD trans but requires a bit of work.
Rangers got the 3.0l Vulcan engines in 1991 model year, and 3.0ls last year in Rangers was 2008 model year
So you can use M5OD-R1 from 3.0l Ranger 2WD 1991 to 2008
Or from Mazda B3000 2WD 1994 to 2007
M5OD-R1 is also called M5R1
M5OD-R2(M5R2) won't work, they were never used with 3.0l engine so won't bolt to the engine.
EDIT:
Reread your post.............auto to manual conversion
Above all applies
Regular cab or extra cab matters for rear drive shaft length, but you can always just get correct drive shaft separately
But computer should be from 1996-1998 3.0l 2wd manual trans Ranger or Mazda B3000
1999 was the first year Ford added PATS(passive anti-theft system) to V6 Rangers, this was part of computer system and prevented fuel system from working if correct PATS key was not used
So if you swap in a 1999 and up computer you will need to add your current PATS keys to the new computer
And in 1999 there were two parts to PATS security, the PATS module and the computer, the PATS module stored and check Key numbers and then activated computer if key matched, PATS module and computer were also a "matched pair" so one can't be swapped unless Ford Dealer does it.
So extra layers of issues with 1999 and 2000
1998 won't have PATS so computer will just work
1996 to 1998 computer should also work OK since computers were also just end users of corrected speed signals from gear driven VSS
1995 can work but it was the first year of the new EEC-V computers and did have issues, 1994 and older won't work, they used EEC-IV computer
You can send your current computer to a Programmer and have the Automatic software removed also PATS if you want, but programmer can switch computer for manual trans use, they can also change other parameters for better MPG or better power as you wish.
No, I don't know one, but there are many out there on the internet, what they do is not illegal or anything.