From one "newb" to another: I test-drove more YJs than I care to remember over the last month and a bit and knew pretty early on that the I6 was the way to go. Like you, mine is a DD, and the 4 cylinder was just lousy on the highway. I'm totally impressed with the I6 — it's a gas guzzler, true, but my mechanic here (who specializes in Jeeps) was pretty adamant that the 4's milage is just about as bad as the 6, due largely to the fact that the YJ has the aerodynamics of a warthog.
On the issue of standard vs. automatic: The standard is a bear in bumper-to-bumper traffic, but it's a hell of a lot of fun to drive. I hadn't touched one in 20 years (I learned on one, but have had autos since), but it took no more than a day to get used to it.
Good luck with your search!