You're definitely going to want to get your hands on a factory service manual for the vehicle. These used to be available from Chrysler. A full set will run you about a hundred bucks, but you're looking at the same exact book the techs at the dealership are using, so it's an invaluable resource. This will give you a detailed teardown procedure, torque specs (for literally every single bolt and screw on the vehicle), which parts are re-usable and which must be replaced, and any vehicle-specific procedures that may exist.
Now for the bad news...
Chrysler hasn't released the FSM's for the 2012 vehicles yet. I don't expect that you'll be seeing too many of these floating around for the next 3-5 years. The most current manual I could find on the Wrangler was the Haynes manual for the 2011-- which used the old 3.8 instead of the Pentastar. While a lot of torque specs in the FSM aren't critical (like trim mounting screw torques), head bolts are extremely critical and torque values must be followed, especially on new torque-plus-angle or torque-to-yield bolts. Unfortunately, your vehicle is just too new to have much in the way of aftermarket service parts and assistance. It's possible to do the swap yourself, Chrysler can't stop you from turning the wrench, but you'll be flying more or less blind and risk making a major headache for yourself. I avoid shops whenever possible (the only things I won't touch are bodywork and alignment, and I'm learning how to do bodywork, but you'll probably still come out ahead of the MSRP of a new 2012 Wrangler even after the service.
