if you are getting used I would go with a 2008 (some bugs were worked out). Also, early 2007 came with a D35 in the rear (depending on model). If you are gettin a 2dr, the one thing I don't like about the 2007 is where the seatbelts were mounted, it makes it a pain to get into or get stuff in or out of the rear seat. Look underneath for scratches and dents. Try to find a cream puff that was never wheeled. Don't be afraid to buy new, Jeeps hold their value so you may not be saving as much money as you think. Especially, after you factor in the warranty. As far as stick vs auto - the war rages on. I personally, like the 6spd, slightly better gas mileage. The auto has an advantage in the mud. It is not advisable to shift the manual in mud, even though sometimes it can't be helped.
2010 Rubicon Silver
Rugged Ridge XHD front Bumper