Hey Patrick!
Welcome aboard the KJ bandwagon! I know how it feels to be waiting for ever on your new KJ. I had to wait nearly two months for my Renny to show up!
As far as your warranty goes.....not to worry. If you want a lift, get it. The only thing they can touch on your warranty is anything to do with suspension...thats it...that being said, most good lift kits come with their own guarantee of performance, so either way your covered.
Go with a 2.5" lift and 245/75/16 tires.....from my experience with my 06 Renny, anymore would be a huge pain in the rear to deal with. I love how mine is set up and handles my local trails amazingly.
To add to the warranty issues, if you can find a good dealer, they won't worry about the lift, and basically pretend its not even there. My current dealer is like that, I get full warranty coverage on my suspension still, even though its modded.
Anyway, let me know when you get your KJ and we'll muster up some of these guys to get out on the trails.
Also there is an up coming new KJ club in the the area, so keep your ear to the ground on that.