The transmission was out of my 13' with 2400 miles on it for a bad 1-2 gear mesh (rattled). I also asked them to look at the TOB becaouse it sounded like it had gravel in it. When I got it back the 1/2 rattle was better but now I had a 4-5-6 (intermitant) rattle. It also pops out of 3rd from time to time and the TOB sounds like it is going to explode when it gets hot.
Now that I've been around and wheeled with a lot more JKs I have learned that the hot TOB noise is pretty normal. (It shouldn't be, but it seems to be.)
My 11' has no issues at all. I think the early 13s had some toubles related to noise but seem to be holding together.
While I have had some issues with my transmission, I would happily buy another stick. I prefer it on the road and I like the challenge on the trail. I am able to "3-foot" pretty well from my road racing days so I don't use, or have a hand throttle. This said, I REALLY need to get my gears soon as crawling does require more clutch work than I would like.
If one is green to off-roading I usually recommend an auto. It is tough for someone who has only driven on the road to change their habbits on the trail.