for the love of god please dont go bywhat jk-forum says, the asshat that runs that forum deletes threads and posts daily that dont agree with his opinions, you'll also notice only his sponsors that pay $2500 a year will get mentioned, no other companies exist according to jkforum. Here you go see what four wheeler magazine says about him
http://blogs.fourwheeler.com/6300609/miscellaneous/fw-is-quoted-and-we-respond/index.html
There are no known problems(I've had my auto for 3 years now, 78,000 miles and been on jk forums for that long) of the trans going bad but there have been fires that the NTSB is investigating, the theory being the trans overheats, hot trans fluid comes out the dipstick onto the engine causing a fire. There is a VERY simple under $100 fix, add a B&M cooler, my trans runs 50 degrees cooler since I added mine. Chrysler's fix was a recall to add a hot oil light on the dash for the 07-08's, 09-11's have them already but that doesnt help the trans cool
The tops leaking has been a problem on every jeep model made, nothing new there, just sucks when you pay so much for a new vehicle and it gets wet inside. They are a lot better at fixing them now, they actually have leak specialist that they will send out if the dealer cannot fix it. I actually have the pdf version of the specialists directions for fixing the leaks.
You can run 35's with 2.5 inch of lift and yes if you have an auto regearing will GREATLY help get your power back. 5.13's for 35s with auto, 4.88 if its 6spd. IF you dont regear dont expect to hold your speed on hills on the highway without downshifting a lot, stock the auto will be fine. IF you get an 07-08 with tow package it should have 4.10 gears which will help if you dont regear right after going to larger tires.
The traction control has to be shut off when you are wheeling, if you are in 4low it is automatically disabled, if 4hi you just press the button for 7 seconds.
The 6spd manuals actually have a lot more trouble then the autos, the throwout bearing is the biggest POS and so is the clutch, almost everyone has noise trouble with the throwout bearing, there is a TSB on it, they get it replaced and it starts doing it again and know one makes an aftermarket yet.
Any other questions let me know and check out
www.jkowners.com