Welcome to the diesel club! I have 3 6.2 trucks, and I have found them to fit my needs quite well. They make awesome daily drivers.
The 6.2 engine is dependable and fairly simple, although it has some diesel-specific quirks that seem odd to some. They're not an overly strong engine if you want to build a drag racer, but in stock form they are a good candidate for a bomb-proof truck build. They won't produce the power of a big-block under any normal circumstances, and they like to spin slow. At 3000 RPM they're not much more gutsy than they are at 1800RPM (and they sound terrible, IMO). A simple mod you can do to increase power output is grabbing a turbine setup from a later 6.5TD engine (the 6.5 is nearly the same engine as a 6.2, over-bored with a turbine and a lower compression ratio). I highly recommend this if your goal is towing. The turbo-diesel setup provides noticeably more power, and I would think it would give a 454 a run for its money, though I've never set them side-by-side. On second thought, I have pitted a 454 against my Suburban (when I was loaded to about 8,000 lbs), and my truck beat the pants off the other one. But that was only because the other truck was a P30 weighing in at 14,500 pounds.
The "stock" 4.56 gears in an M1028 (w/o overdrive) are not well suited to a 6.2 diesel, unless your goal is low-speed crawling. On the other end of the spectrum, my K10 has 3.08 gears, 29" tires, with overdrive. 55MPH is about 1400RPM, and 65MPH is about 1625RPM. This is about perfect for non-trailer driving. My Suburban has 3.73 gears, 31" tires, with overdrive. 55MPH is about 1550RPM, and 65MPH is about 1800RPM. This is about perfect for trailering (although I think it's too much gear for how I usually drive it). If you were able to get 33" tires underneath the M1028, 55MPH would be about 2550RPM, and 65MPH would be about 3000RPM. Doable, and obviously the M1008-series trucks all came that way, but they really aren't happy at highway speed.
One other benefit to keep in mind is that 6.2 engines are capable of really good mileage when set up properly. That K10 with 3.08s will regularly pull 23-24MPG at 55MPH, and 21-22MPG at 65MPH (sometimes higher). So the potential for a (relatively) cheap daily driver is there, if that's what you are interested in with this stockish vehicle.
I wouldn't worry about the NP208 if you aren't abusing the truck off-road. Plenty of folks hit trails of all types with NP208 cases.
Problem areas: I don't think the engine has any particularly troubling issues, just a few quirks. If you run a mechanical fuel pump AND suck an air bubble in your fuel line you are stuck cranking the engine until the bubble passes (there are procedures to help both avoid and resolve this). Glow plug controllers often fail, but they are easily fixed, or even more easily bypassed (I wired up a momentary-contact switch on 2 of my trucks). 6.5TD engines under heavy trailer loads can overheat and crack heads (so buy a pyrometer if you go with the turbo setup). Square fuel filter assemblies can sometimes leak (though mine never have). Glow-plugs burn out (particularly older-style plugs), and the engines are hard (or impossible) to start without them. Low-temperature starting may require a block heater (pretty sure you won't encounter that in South Florida). Overall these engines don't have much that can be messed up. Outside the injection system they are dirt simple (and the injection system isn't bad either, it's just different). The only electrical requirement is a single 12V wire run to the fuel-shutoff solenoid on the IP. The one piece of smog equipment (EGR) will already be gone from your military engine.
The military trucks have some wiring differences, but other aspects of the trucks are identical to civilian models, though they are stripped-down models.
Wiring differences include:
Blackout lights (marker led lights on both bumpers and a small covered headlight in the grill)
A second ground-isolated alternator
The truck's two batteries are attached in series instead of in parallel
Starter motor runs on 24V instead of 12V
Glow plug controller operates on 24V (but plugs still run on 12V).
24V jumper cable receptacle installed in grill
Everything except the starter and the input to the glow plug controller operates on 12V. Aside from the 2 extra switches, ammeter, and dual generator lights on the dash, the truck is like any other Chevy diesel truck.
These engines are often a love-or-hate relationship. If you want speed and high-end power, this is not your engine. If you want high mileage this is just about the best thing out there. For everyone else (in the middle), the engine is either
weird,
noisy, and
smelly, or
awesome,
torquey and
cool.
