I think about the only way to figure/find out is to just start tearing into it and put it in there and see what kind of room you have for things.
I think you'r major problem is going to be the rear driveshaft angle using a divorced transfer case,those things have a major short wheelbase so there is not much room for drive line angles unless you drop the whole angle of the driveline to help with the short driveshaft angle,but that also causes less ground clearance..short driveshafts with bad angles on something like that causes vibrations and serious strains on the driveshaft and rear yokes,causing failure quite often.
And being a young guy he will probably want a lift to fit some bigger tires under it too,there goes more driveline problems from the increased angle...
I know about this first hand because i currently have a 95 YJ Jeep Wrangler i have had for quite a few years and planning a FI 5.9 mopar into it and us jeep owners have the same issues when upgrading the drivetrain,but those Samurais have an even shorter wheelbase than the Jeeps so the problem would be the same if not worse to correct.
Alot of guys go with manual trans because they are so much shorter than the auto's,but i like my auto,much nicer for daily driving and much better for control in the mud,rocks and trails.
I am not discouraging you from doing the whole thing,just shedding some light on some of the problems that need planned/solved.
Those Suzuki Samarai's have a big following because of how light they are because they do well in mud and trails,find a good forum for them and search and ask there... i'm sure someone has done the same swap as you are trying to do because the 4.3 V6 is a very popular swap into Jeeps and small 4x4's because of their dependability and power