I just put my RE transfer case drop in last night. I, too, read up on this and decided to do the double-nut method. At first, my nuts were too soft (enter joke here) and I had to go to Ace Hardware for some harder nuts (enter another joke here).
Those nuts seemed to do the trick as I was then able to cinch them down nice and tight without rounding the nuts off (not really worth a joke, but go for it anyway).
I began working the nuts nice and slow (oh man, that was a good one) and moved them back and forth. First a bit loose, then tightend, then a bit more loose. Once you begin loosening the stud with the tightened nuts, you'll get the feel of it and will know when you can safely back the stud out without shearing it off inside the unibody frame. That will mean drilling and tapping, which you don't really want.
I also found it useful to use an extractor used for rounded heads and studs. I had to remove the nuts and jack the transer case back up first to gain more access to the stud, but it worked well.
Enjoy and be glad you are working on your jeep with your nuts intact.
-- Project Old Blue
99 Cherokee XJ Sport
RE 3.5" Super Ride lift
BFG's
lots of extras