Assuming 2WD not 4x4
M5OD-R1(M5R1) is the manual transmission's model number for Rangers 1988 thru 2011, but NOT what it fits
Bell housing on each M5R1 was/is specific to only one Ranger engine model
M5R1 from a 4.0l or 2.3l engine will not fit on a 3.0l engine, or visa versa
So you need an M5R1 from a 2WD 3.0l Ranger or Mazda B3000, 1991 thru 2008(last 3.0l Ranger) will work
Obviously later years should have less miles/use
In 1999 you don't need the speed sensor
Clutch pedal assembly, 1995 thru 2006
Clutch Master
Clutch kit and flywheel
You will need to connect Reverse lights, the 2 wires are there in automatic wiring harness, just need to cut them and splice to reverse light connector on manual trans
There is also a Neutral Safety switch to prevent starting in gear, you can jumper these 2 wires or run them to a clutch switch inside the cab
Your 1999 computer has software to control the automatic, so computer will turn on the CEL(check engine light) unless an automatic is connected
This will not effect driveability, just the CEL will be on all the time
1999 thru 2011 Rangers have PATS(passive anti-theft system) which is in the computer and in 1999 there is also a separate PATS module
Computer and PATS module are "married" at the factory so one won't work without the other
So swapping out computer for manual model is not all that straight forward, but certainly doable
You can't buy new "sets", they were never sold that way, Ford Dealer can "re-marry" if computer or PATS module fails, but they usually won't do that any more
Best bet is to look in wrecking yards for 1999 3.0l Rangers/Mazda B3000 with manual trans, 2wd or 4x4 doesn't matter for this
Buy the computer AND PATS module(above glove box), they are already married and its plug and play
Also get at least 1 PATS key and its ignition cylinder from steering column of same truck
Then you can swap it all out and have a running manual vehicle with CEL not on all the time