I was considering doing an automatic behind the 5.9 in mine, but it was cost prohibitive at the time. The Allison 1000/2000 series can be had with an SAE2 or SAE3 bellhousing, and parts are available to bolt them right up the the Cummins. In fact, my engine had one behind it when I bought it, but I couldn't afford to buy both at the time. There are standalone wiring harness and controller kits available to run it behind a manual engine and the kit cost is around $1200. The 2wd Allison is also only marginally longer than the Spicer 3053A, and while I didn't go so far as to measure it, I think it could be installed without moving the transfer case back. You also get the benefit of a six speed automatic here if you get a 2006 or later transmission.
The NP205 will probably hold up especially since your truck is bobbed, and there is a boatload of aftermarket support and upgrade parts available for it, including input and output flanges that will bolt right to your driveshafts, heavier mainshafts, etc. This is not a bad choice, and I have considered it myself.
You will lose the park brake though, so be sure that the transmission you get either has a park pawl in it, or have one installed. Many of these transmissions, especially those from medium duty applications that come with SAE bellhousings won't have a park pawl in them, so if you use the 205 you'll have no way to keep the truck stationary when parked.
It is also worth noting that I haven't broken my 3053 yet, and even the Waterloo 5th gears are holding up fine. I figured if I was going to break it, I would have already. I have been in Korea since late March, but I put quite a few miles on it before I left and I'm not exactly easy on it.