You can't go wrong with a 3.73 rear axle. I have it and love it. Pretty good fuel mileage and tons of traction and great aggressive feel. Think of it this way, you're not buying a Grand Cherokee Laredo with a 3.06 or a Ram 3500 with a 4.10, you want to get a bit of both.

I can't comment on size of lifts or tires etc. but we won't "void" your warranty but what will happen is that if any of your aftermarket components cause an issue with warrantable components, all those related repairs would be at your cost.
You can also refer to your warranty information booklet under Non-Chrysler Modifications and Non-Chrysler Parts, you'll get a bit more of an explanation there.