You're talking about a large job.
It's not as simple as "swap and go". Unfortunately. When doing something like this you would need to have fabrication skills (Welding and minor metal working skills). You would need to be very familiar with automotive electrical and or know people that are. You will need a good steady hand and geometry skills so everything lines up perfectly once you're ready to install it.
The ECM and wiring loom will have to be replaced with either a completely custom ECM/Loom or you would have to use the loom from the engine you're swapping into your Trooper. You could theoretically pull the loom and ECM out of a car that has the engine you want and put it in. Personally I would just buy an entire custom ECM and loom.
Depending on what your putting in it you may need to move the firewall and actually re-engineer certain things under the hood to get the results you want. The ECM and TCM will freak out if you try wire up the swapped loom to the stock ECM of the Trooper.
As far as your transmission goes, there are companies that make custom bell-housings to mate up transmissions to just about anything. As far as electrical involving the transmission, you'll need to consult with a factory diagram of it's wiring and go from there.
I've worked with guys on projects where they swap motors in and out of little race cars and it's a very long and tedious process if you want it done right, but if you take your time and learn as you go you'll be good to go. Just do as much research ahead of time so it doesn't go from a project to a pain in the butt. Good luck with it.