As I understand it there is a general rule of thumb; all warranties will be good for items not changed, It gets tricky with things connected to your upgrades.
What I am trying to say is that if you lift your rig, the shocks and springs will not be covered if you put new ones on (this is obvious). If you have a problem with your transmission, well that couldn't have been effected by the lift so it would be covered. However, if you have problems with your drive shaft and U-joints, it could be argued that they were damaged by the lift so you will have to negotiate.
I would recommend that if your Jeep is under warranty and you have modifications done that might affect your dealer's warranty, then make sure you have a separate warranty from the place doing your mod or the vendor selling you the parts, to cover the modded parts and any damage caused by them.
I have never bought a new Jeep so hopefully someone with more experiance will chime in.