I have a '91. 5 W-250, in which I had an ATS Heavy-Duty transmission w/ Triple-lok torque convertor, installed. It has worked flawlessly, towing a 25' travel trailer in the mountains of the West. (I realize I'm not towing anywhere near as much as you. )
A few years ago, I purchased an '03, 3500, HO, NV-5600, 4X4. I've towed the same trailer throughout the same mountains.
Personally, I prefer the stickshift for mountainous towing due to the greater selection of gears. If I was doing a lot of towing, it would be my transmission of choice.
If most of my driving was in town, stop & go, rush-hour driving, the auto would probably be my transmission, of choice. The ATS seems to be very rugged & inspires confidence while towing. It's no sloutch!!!
Another issue is the costs involved. The auto costs more, to begin with, than the stick. Then, you have to invest many thousands of dollars to create a transmission that is as durable, as you need. Lots of extra expense that you can avoid by purchasing the stick.
But, if you really hate the way the trans. shifts, then the auto is the way to go. Also, if the extra costs don't bother you, then the auto is the way to go.
I've heard nothing but good things about Goerand's transmissions. I can't imagine you would be making a mistake by dealing with them.
Best of luck with your decision.
Joe F. (Buffalo)