Personally, I think I would go with the Stak and I would only chose the 2-speed. For about 400 less than a 2-speed Atlas, you can get the Stak 2 speed which more directly fits the Bronco. I have not read anything negative about the Atlas or Stak, but for the price difference and what I have read about the fit of a Stak, I think it is right for me.
I originally planned to do the JP rock-eater 4.86:1, but it would cost more with the rebuild kit, gears, and shafts to go that route vs. a Stak. I have never liked the idea of stacking boxes, due to driveline angles and input shaft stresses, but it sounds like it works for a lot of guys.
I had thought about the 3 speed, but I cannot see why I would need it. With a auto, the various speeds of the trans, and a 2 speed t-case, it seems to me that all of the gear ratios I need would overlap. Maybe some need it, but I could not justify the cost....speaking of cost, it's gonna be a bit before I can afford the swap:-[ Somebody needs to start a mass buy on the 2-speed Stak;D