I feel for you man, but you let this happen to you unfortunately. First of all, you let this go FAR FAR FAR too long. After the second attempt, I would have had my lemon law attorney on the phone, threatening them. After the 3rd time, proceedings would have started. There is NO WAY I would eat this BS from the dealer. The "rear diff was replaced." WTF does that mean? The axle? There is no "diff" in a rubicon. Did they replace the locker? My jeep dealer is fairly cool, and their service manager told me point blank...when it comes to warranties (chrysler's dime) "we don't waste time repairing anything. They don't "fix axles." They order the entire assembly in a crate from chrysler and slap it on. Saves them a ton of money (to slap an axle on is a lot faster than doing surgery in the guts.) The driving out of state...what BS is this? I'd drive their loaner into a tree if I heard that BS.
Get your lawyer to start moving. Too many things (brought it in for a locker and now your tranny sucks) are wrong with it now, so the only acceptable solution to you would be a full refund (having chrysler buy it back) or a brand new 2014 Rubicon. Oh, and there are laws regarding payments. If your vehicle is out of your possession for too many days out of a month, they eat the payments. A friend of mine had BMW eat 6 payments (3 actual and 3 courtesy)...and in the end, they bought the 5 series back (bad diff).