You said it... I am probably buying a 2001 dodge 1500 very soon and I have been doing hours of research on it.
I started to get very nervous upon reading all the bad stories about that truck, but then you have to realize that the old saying is true : If someone has something that is good they will tell 2 people, if someone has something that is bad they will tell 200. For all the hundred thousand or so trucks there is bound to be some defects, just like all the auto companies... It doesn't mean that ALL the trucks produced of that model are bad... You just have to do your homework, inspect the truck, and it is probably a good idea to get an extended warranty...
I recently bought a 2001 Dodge Ram SLT. Came with a 5.9L powerhouse and an auto tranny. I must say that it has impressed me very much. I was extremely surprised by the off-road ability of the rig. With A/T tires I went four wheeling and didn't even think of getting stuck. The only time any mud/water came into the cab was when I was in a mud hole that came to the bottom of the window. Something got wet and it ran rough for a couple minutes, then was back to being a beast. Had the PCM flashed a day or two after I bought it. I think the previous owner tinkered with the programming causing it to ping at high RPM's, the reprogramming fixed this. I've never cold started a vehicle that didn't run rough until warm. That's a normal thing. I've noticed a lot of people posting about cruise control problems when going through "hilly" terrain. O/D is made for level ground, not hills, that's why the constant shifting of the tranny. Take it out of O/D until you are clear of the hills and you shouldn't have a problem, that could also be a contributor to premature tranny failure as well. Change fluids more often that the book suggests, and all should be well.