'88-'91 Troopers have power disc brakes and a hydraulic clutch master cylinder mounted right there on the firewall.
I woudln't be surprised that the bolt pattern of the pedal box isn't all too much different than the one for a MUA5 trans with hyd clutch.
There's no difference in the size of the engine compt of an '87 Trooper than there is in the compts of a '88-'91. So things are gonna fit, even if they're tight.
Do you have any yards near you, where you could take a picture of a later-model Gen I to see how it looks?
If all the brake and clutch parts are removed, you could even make a template of the firewall. This might help you in transferring bolt holes.
Look at it this way, to do anything you've got to remove the existing pedal box. Once removed, compare the 2 pedal boxes side-by-side. You'll get a good sense if there's anything radically different.
You may even have a few bolt holes that line up. That'll help immensely with the mod. Bolt up the MUA5 pedal box and see what it looks like.
Anyway, that's pretty much how I'd go about it. You've got to pull what you're changing, compare to the new parts, check the fit, do what you need to do to make it work.
IDK how the (2) studs for the hydraulic clutch are attached to the firewall; they may be spot-welded, pressed-thru, etc.
Once you've mounted the MUA5 box in its new home, unscrew the "yoke" off the end of the clutch master cylinder's pushrod. That yoke fastens to the clutch pedal with a pin. Temporarily mount the yoke on the pedal (in its normal position, with a bolt that's about as long as the clutch cyl push rod you just removed the yoke from.
You can position the clutch pedal yoke and temporary bolt, and use the bolt as a guide to mark a center-hole thru the firewall. Very carefully lay that hole out, measure as you need to. Then drill a hole and see how the bolt aligns into the engine compartment. If you just drill a small hole for the bolt, you'll have room to adjust the center of the hole once you make sure the bolt lines-up well going thru the firewall & into the engine compt.
You might have to file or grind the hole out one way or another to get it lined up so it's going to hit the plunger on the clutch master cylinder, straight-on. That's the critical thing.
Once you have the center of that hole perfectly positioned, enlarge by grinding until the larger-diameter part of the master cylinder will fit thru the hole.
Then, with the clutch master cylinder strait up-and-down, you can use the holes in the mounting flange to lay out the mounting holes in the firewall.
After that, all you need to do is figure out how to bolt it to the firewall! One way that would be pretty easy is to use a "Star" washer between the bolt head and the firewall. Insert that bolt thru the firewall, from the inside. When you tighten the mounting nuts on the engine compt side of the clutch cyl, the star washers will "bite" into the bolt head and the firewall sheet metal, keeping the bolt head from turning. Then you don't even have to have a wrench on the inside.
Ideally you could tack weld the bolt heads to the firewall. That's pretty handy only if you have a welder, and it's pretty tight in there so you risk damaging other components when welding.
Or, maybe the clutch pedal pushrod will line up with the old clutch cable hole. I wouldn't be surprised if it did. And the Power brake booster may fit the spot occupied by the old one.
Anyway, that's more-or-less what I'd do. It's a process of discovery, you dig into it, then lay the new part in where the old part was, and see what it's gonna take to get it in there. It helps to have an eye for that stuff, but that comes with experience.
Once you get the old pedal box out, stick 'em side-by-side and take a pic. Post a few different shots here and we can all scratch our heads together about "What Next".
Hope that helps, you just gotta dig in there!.............ed