It would be best to buy a donor pickup with the manual trans in it. Then you can swap all the parts you need over. You are going to have to change the pedal assembly, mount the clutch master and reservoir, and possibly swap the driveshaft over also.
Absolutely the best way to go. I've done this conversion on a '90 Bronco II, with a '90 Ranger for the donor truck. Another item on converting a '91 is the column shifter for the auto.
The needed parts' "short list" includes the transmission, a flywheel, brake/clutch pedals, a small underhood wiring harness, the triple function switch with mount, correct computer*, steering column (or its parts, including the cluster PRND21 display blocking plate), shifter boot and correct floor plate.
If you're going to do this, it's best to just buy all new clutch parts: disc, pressure plate, pilot and throwout bearings, master and slave cylinders and a new fluid line (I used, and recommend, the Perfection Clutch pre-filled master/hose/slave kit). I spent just under $250 for all of these parts new, and that figure includes having the flywheel surfaced.
With a donor, parts would be removed at your leisure, and to boot you'll have a "Chinese blueprint" to see how everything went together originally. But keep in mind, you have a 2.9L; with a 4.0L donor, the clutch is larger (9" versus 10"), you'll need the donor's starter, and *I don't think that the 4.0 computer will be useable with your 2.9. Your auto computer will work, but it'll throw a light and codes related to the missing auto. The lower gears on a 4.0L manual are a little "taller", but are still workable behind a 2.9. In my case I hunted until I found a 2.9L donor.
You'll need the parking ("emergency") brake with a manual. If it won't hold the truck now, it's good idea to do the rear brakes, too.
Finally, and don't take this the wrong way, you can cut a lot of corners, and still "make it work", if you're OK with that. Or you can research what's needed (tons of info here on TRS for the searching), get your parts lined up, and then it's really easy to do the conversion so well that it looks factory-installed. Good luck!