If you could find a dead 2.8 Trooper or 4WD 3.1 Rodeo/Pickup with a 5-speed, there's your parts for the swap.
You could build a 2.8 into a 3.1 as well, with the proper crankshaft and pistons. You can also use bolt-on performance adders for even more hp and torque.
Since your '86 is carbed, you could do a very simple installation and use a V6 TBI intake manifold, with a 2-bbl carb. There are adapters out there that will bolt up a Holley 350 or 500 CFM 2-bbl carb to a TBI intake.
So you'll just use the stock 2.8 or 3.1 TBI intake and the adapter, and away you go. No pesky ECM or extra wiring to mess with. Bore the intake manifold inlet holes to 1-11/16" for better airflow.
You'd also need a non-electronically-controlled distributor, just look for an early S10 dist, 49-states, with vacuum and centrifugal advance.
You'll have to switch to hydraulic clutch actuation to run a newer transmission. A parts rig could supply what you need, far as pedals, master/slave cyls, and piping go.
Definitely upgrade the rear end, too. '88-'91 Gen I. V6 or 4-cyl, doesn't matter. As I recall our Isuzu Meister Jerry Lemond said the only issue was emergency brake cables. You may need to install an aftermarket universal set, such as you see being used on many classic cars.
If you use a '93-'95 Camaro/Firebird 3.4, you'll want to upgrade your exhaust for sure. 2-1/4" is free-flowing while retaining low-end torque. A 2.8 or 3.1 will like that size, too.
Instant Update: I found a file that I had saved with Jerry's comments on Gen I rear end swaps. Note the E. cables mention, sounds like not a big issue. Jerry is a Treasure and a veritable Fount of ZuZu knowledge!
84-87, with drum brakes just locate an 88-91 Trooper that did not come with the big tire package and it will bolt right in, you will have to make a minor adjustment in the parking brake cables, their hookup in the frame is diff, but easy to fix.
85-86 the rear of the rear drive shaft will have to be changed, just the yoke flange; on the 87, the rear shaft will need to be shortened about 3/4 inch not much at all.
Flanges are the same, master cyl and the brakes all bolt rite up. Only exception to this would be by chance if you have an 87 turbo dsl, won’t work, as it was the only year Trooper that came with a 4.11 gear ratio, to slow down the eng speed at road speed.
All other year Troopers came with 4.55 except the ones that had the big tire package 89-91 and they were 4.77, but they are extremely hard to find. Jerry
Good Luck with the project, keep us posted!...........ed