If you aren't familiar with gear installation, we recommend you have a trained professional install them for you. Gear set-up isn't the place to learn basic mechanics.
One of the most common mistakes we find enthusiasts making when they modify their vehicles is that they neglect to change out their gearsets when running oversize tires. In some sense this is understandable due to cost, but in most instances you can buy the gears and have them professionally installed for less than $1,000. Swapping to the proper gear ratio significantly puts the factory performance back in any vehicle.
There are some minor changes in the JK's Rubicon axles. We really like the fact that Jeep included oil add and drain ports. A second change is the electric-locker connection, which is not difficult to disconnect. We suspect that if you are going to swap out your gears you know what you are doing, so we're not going to get into a full gear install.
We have run Superior gears on numerous project vehicles and can honestly say we haven't had a single problem with any set. So to bring your mileage and vehicle's engine performance back on track with factory specifications, we highly recommend you swap out your JK's gears after installing larger-than-stock tires on your new Wrangler.