The most practicle solution for your swap, since you have a complete pickup,is to swap the entire engine, tranny, wiring harness and everything else in the drive train from the pickup to the Trooper. Other than the drive shaft lengths it should be a fairly simple swap. But,the down side is, unless the pickup is 4WD you'll lose that option.
The pickup motor will be a real slug in the heavier Trooper. There are several guys here who have added the C223 Turbo system to the Non-Turbo Motor with some sucess but it's a gamble that the engine will live very long with the blower on it. You see the rods are weaker on the non turbo engine. An important fact!
If you want to use the pickup diesel motor with your MAU5 then you'll need the very, very rare front half of the Diesel transmission. Hard to find because once the front half is removed the rest of the tranny is pretty much useless. In theory, you could put the diesel tranny in your Trooper but it mounts all different. So fabrication skills are needed. But, should you be able to get your hands on the front diesel housing it will bolt right on the MAU5 Trooper transmission. With the tranny on the bench it takes about 10 minutes to swap. "IF" you know what your doing. I can send you pictures of one of these, if your interested in seeing the diesel housing I'm talking about.

There are some other options, but none of them cheap or easy.
One of these days you will be able to slip in a Mercedes 300 TDI motor in your Isuzu and have all the GO you will need. That's my hope anyway. But I'm still a year or two away from having that ready for the market. <img src="/forums/images/graemlins/frown.gif" alt="" />

We've covered a lot of this before, so an extensive search will give you plenty to read upon.

CJ