I'd pass on the 12-bolt. You don't want a welded carrier (if I understand what you're doing), the water contamination means it's due for a good cleaning, and I personally would avoid running 3.73 gears with a 6.2 on stock size tires without overdrive. Especially if you don't have a reason to swap out the front, I'd stick with what you already have. If you're hoping for decent road manners with a 6.2, keep the cruising engine speed around 1800RPM. Personally, mine doesn't hit 1800RPM until about 75MPH (3.08 gearing, 29" tires, 0.70 O/D transmission). That's a bit on the anemic side, but you're on the other end of the spectrum. In stock form an M1009 hits 1800RPM around 55MPH, changing that to 3.73 gears brings the sweet spot down to 45MPH. Even bumping the tire size up to 33" only brings that cruising speed up to 48MPH. So if you switch to 3.73 gearing you will be overspinning the engine on the highway. In my opinion, these engines get loud and obnoxious when the speed climbs, and the fuel economy tanks. So I don't see the benefit of gearing down unless you want lots of low-end grunt. It has its place, but my bet is that the mud truck in question wasn't running a low-speed diesel engine.
P.S. - The gearing options are detailed in that chart that I posted earlier.