When I was shopping for a new, er,.. jeep, I priced them out and ended up buying a new one. As stated previously, they hold there value really well. I just saw a 98 Tj 4 cyl the guy is trying to get 8 grand for it. And there are no shortage of 08's selling for 21,000.
And from what I have read, in many posts. They will only void the warranty will only be voided if the failure is related to the lift.
I had mt head done at 40,000 and the warranty was honered. And I am sure it depends more on the dealer too.