I've had several Sammys (somewhere around 8 of them...lost count though) and have modified them a fair bit, including one with a modified GM 2.8 V-6. Most were running 33" rubber, although my buddy had 36" Swampers on one. I'm a firm believer in matching an engine to the vehicle, although you can get away a little by matching the vehicle to the engine. Personally, unless you are going to do what Crewcab59 did and stretch the wheelbase a fair bit, extend the nose a little, and swap in larger axles (you did mention 44s), I would find a smaller, lighter engine. And as someone who has owned Samurais with various amounts of modification, for 'wheeling, you can't beat a nearly stock Sammy set up with a good suspension.
Once you start playing with the wheelbase more than a few inches, swapping in larger (and heavier) axles, engine, and t-case, you end up with something that is the size and weight of a Jeep. And a Jeep has nothing on a Sammy off road. I've owned both, and even my wife has commented on how much better the last Sammy I owned did. My current trail vehicle is a '98 Cherokee XJ with lockers, 31s, (will be going higher, it used to be my wife's vehicle, and she had to be able to drive it), a few custom suspension mods for more articulation, and a couple other things. Although it does very well off road for a vehicle with 31s, it has a much tougher time in our New England terrain than a stock Samurai. A Samurai almost floats over deep, thick mud; it will happily go through water over the hood if you set up a home-brewed snorkel; it will skim over rocks that hang up heavier vehicles; and it will out turn and maneuver any other 4x4. Add weight to it and it will sink in the mud; it will hang up on rocks much easier; and a much longer wheelbase will screw up the turning radius.
Another thing to look at is the weight balance. A Samurai is very light in the front, and is just as happy going up or down a steep hill. Toss a Cummins up front, and it will want to tip on it's nose. Having a much longer wheelbase will help, but then you get back to losing the turning radius.
All of this is based on the terrain we have here in New England- lots of ledge, thick mud, deep water, washouts, steep hills, and very tight trails. Depending on where you live some of what I said won't matter. If I didn't need the extra room for camping gear for two of us, plus our dog, I'd still be 'wheeling a Sammy. Someday I'd like to build another just for local, New England use, and use the XJ for longer trips involving camping.
Just think about what its going to do to a 2050 pound vehicle (the hardtop is more like 2150) if you yank a 100 pound engine and install a 750 pound one.
Jim