Michael and I were trying to post at the same time. You need to think about the fact that you are dealing with a vehicle that is 23 years old and is probably worth $1500, tops. If you can do all the work yourself you are probably looking to spending $5000 or more on parts. This may sound like blasphemy on this site, I would recommend that you sell your Trooper as is, add to that money what you would have spent on parts and buy a CJ or YJ. It is clear from your questions that you are dealing with a dream and haven't done any research. We all have done the same thing.
Michael has taken his 'Pup about as far you can take one and still be IFS. I have what is most likely the first 2.8 converted to a 3.4.

By the way, your Dad's T5 and tranfer case is a driver's side drop, and yours is a passenger side, so you are talking about an axle change in front so you can another $2,000 at least to that option.

Isuzu didn't transplant the entire V6 drivetrain to the Trooper, just the engine, and that was actually a lot of work for the factory.