yea the 3.73 are stock with 410(or 411, cant remember) as the option. Most guys say the 410 are NOT that much better, especially if you plan to go to like 35" tires and swap gears to 4.56 anyway, just save your money. I couldnt find a dealer within 50 miles either that had a Rubicon with 410's in it, they were all special order.
I went with a hard top only and got a Spider Web Shades sun shade for when the top is off. I didnt get the factory soft top at all since I think its a $1295 option which is ridiculous. Its a nice top, dont get me wrong, but there are a LOT of aftermarket soft tops that are just as nice for 600 bucks. The Spider Web Shade cost all of $99 I think. I also keep a Jeep Rain Coat from from JeepCovers.com in the back when I dont have the top on. Takes about 3 minutes to put it on(after the 20 minute first time) and its water tight. My jeep has sat in a few overnight rain storms while out on the trails camping and was bone dry in the morning. I think the rain coat was 129 bucks or something and really well built.
The JK's are SUCH a big improvement over the TJ's its not even a comparison. I have gone one some crazy trails in my basically stock Rubicon(I only have a Currie Anti Rock on it for now, but I am collecting parts for a 4" lift, 37" tires, high steer, etc..., but its a long 10k dollar proposition so I have to space out the parts purchases).