Well Radar, as the former owner of a 1991 DTD with auto, a 1995 DTD with auto, a current 1999 DTD with auto, and now the owner of a 2003 DTD with 6 speed I think I can make a few comments.
First, all my DTD's were great trucks. I didn't sell them because they were bad, but because improved models became available.
When my wife and I began fighting over who got the truck the only solution was to get another.
Most anyone here will tell you that the DTD with auto is a great truck, but the stock auto has some limitations. If you are going to tow some serious weight (say over 8,000 lbs) given time the torque converter will die and other elements of the transmission as well. There are companies like DTT, ATS, and others which market aftermarket upgrades to both the transmission and torque converter that increase reliability and the ability to put serious horsepower to the ground while towing.
Because I was towing a big fifth wheel that would ultimately make me spend some big money on my transmission, and the wife only pulls a small horse trailer it made sense to let here have my old one.
I do like my '03 very much. It is super quiet, has abundant power, and the transmission is geared just right with the 6 speed mated to the HO engine. I think I will still add an Edge fueling box when they become available because you can't have too much power.
Please don't take my response as implying that the auto is a bad transmission. It's just that we all tend to bomb our trucks, and when adding a heavy load they just don't tend to hold up real well. If you keep the truck stock and stay reasonable with the tow weight (+/_ 8,000 lbs) you'll do fine. The problem is you'll soon be yearning for even more power and then you bump against the transmission thing again.
Good luck with your choice. Either way, IMHO, the Cummins Turbo Diesel is the most durable and reliable engine in a 3/4 ton truck today.