Read this: http://www.jeepforum.com/forum/f9/i-...-my-tj-751873/
. Running 35s is a pretty significant commitment. 33s a lot easier.
As to your specific questions, those stock wheels have a lot of backspacing and are probably going to be a problem for you as tires get bigger. Can potentially be addressed with spacers, but most go to aftermarket wheels with less backspacing.
AT v. MT really depends on your usage. Unless you tell us a lot more about what you'll be doing very hard to give advice.
The thread I linked above will tell you a lot about what is required to get to the 35s. For specific lift manufacturer recommendaitons go to TJ Tech, search and read. Hundreds of "what lift should I get" threads.