I used the scx10 for the base for my jeep build. Very happy with it and lots of upgrades for it now. Like Chassis mounted steering. You can also buy leaf spring kits for it. Im about to put leaf on the rear of mine.
Another choice is the axial honcho kit. This just has an extra inch of wheelbase over the scx10. The honcho is 12" I think. Depends what wheelbase you are going for.
As for battery and controller. I just use 2s lipo's and a TQ3 controller. I use the 3rd channel for my winch.
One good upgrade you might want to get when you get the kit, is new shocks. The stock plastic ones are junk. I use the proline 90mm shocks. Smooth as.
Stock gearing is good. I use a 30t motor and this gives the truck good top end speed but still crawls. But a good speed controller makes all the difference too. Look up LRP. They have awsome speedy's. You can setup braking, accelaration etc.
Also saw one of the Jk shells on ebay the other day. They are hard to find.
Hope this all helps. Pm me if you need more info.
Kizzo