It is a major undertaking. See the link in my signature for a journal of my progress. I am about 90% completed after nearly 3 years of work (off and on). Projected completion date is sometime this spring/summer.

I don't want to discourage you, but better fuel economy as a short-term goal doesn't make any sort of financial sense. If you add up the cost in parts (and especially time - you'd be the first to do this with a Trooper that new, so all the research would need to be done by you beforehand; also the time involved in actually performing the conversion), my guess is that you'd be far ahead to just keep buying gasoline for your current engine for a number of years.

Running biodiesel and not purchasing foreign oil are good goals, but not cheap ones.

The newer Troopers are not as spartan as the older models and may not be as easy to work on, although I have no direct experience with this. I would guess that the wiring would be much more difficult to deal with.

You would also need to be comfortable with all aspects of automotive work, including major work on all vehicle systems, as these conversions touch every part of the vehicle. Lots of tools and a space to work are also required. Metalworking abilities are also needed.

You'll have to decide for yourself whether this is something you want to take on. The forum can provide a lot of help if you decide to move forward.