Welcome to TRS.
You've already made two good moves; getting a '90 Ranger, and looking at converting it to manual.
Check out the "Articles / Resources" link in the upper part of the page. Lots of good info in there. And, there is a ton of info you can find by using the "Search" function on this site.
The '89 parts truck is a good find; it's useful for all of the "annoying little bits" that you'll need. The clutch pedal assembly, steering column whole or parts, the wiring harness for the manual trans, and the floor plate and shifter boot. Unfortunately, chances are it will have the Mitsubishi FM-132 5 speed manual. For a 4.0 application, the Mazda M5OD is the preferred transmission. Even if it's still good, the FM-132 will "work" (i.e.- bolt up), but it probably won't last long with the 4.0.
You'll need a flywheel, clutch, and the hydraulic clutch parts. I'd suggest buying these new as good name brand, like LUK, and do yourself a favor and get the master / slave cylinders as a pre-bled set.
You current ECM will work, but it will have fault codes for an auto trans that it won't "see" anymore. The best option will be an ECM for a 4.0 with manual (you'll need to determine EGR or non-EGR).
What you are wanting to do, is easily done. There's a few quirks, especially for a Ranger noob, but you'll get good info by posting questions here. A lot of it is going to be determined by how you want to do the conversion- whether you want the minimum to just get it done and make it work, or if you want a proper manual conversion done so that all of it looks to be factory-installed.
Good luck!