Transmission is stock. I have NOTHING but good things to say about it. The only issue I EVER had was when I had a defective juice module, when it overheated it shut down, and the trans shifted erratically. Not the truck's fault though, and it to this day has no reluctance doing anything I ask of it. The only issue I see developing is with my dfuser extreme race tune. The 3 to 4 shift has to be either under WOT, or light throttle. Transitioning between them is a no go. If you go from wot, and let off before it shifts, it will bang 4th to the point of chirping the 40" tires. Not good, but definately in the tuning. My Innovative tune doesn't do this, and is preferred for this reason.
It should be noted that although I'm more abusive than most, if my truck develops so much as a shimmy, leak, or noise, I don't sleep until it's fixed. I have 284k miles, and JUST under 5600 hours. I have an 06 with 101k that has 4800 hours on it, and it has been MUCH more problematic to say the least.