Carolyn - 'm coming to this thread a bit late, but I feel your pain. I am in Denver and try to get up to the mountains about once a week. I am on my second JKUR, after trading my 07 when the 12's came out. The door hinges on the rear doors were beat to hell. With my '12, I removed the rubicon rails and installed some sliders that extend out farther. So basically, whatever gets kicked up and thrown by your tires, will get blocked by the bottom of the rock rail. You could even go with aluminum rails like the ones from Nemesis; I've toured their shop here in Denver and they make some really nice, expensive parts. Their rock sliders are all aluminum. Now I know many will go poopoo to aluminum, but unless you are doing all rock crawling, these things will last forever.
Couple other thoughts...when its time for new tires, the Cooper Discoverer STT is an amazing and the best M/T tire I have ever driven in the snow. I can go anywhere on I70 in 2 wheel drive in a storm. Oh yeah, they also last forever...like over 50,000 miles with room to go.
I wouldn't be too worried about the under of the jeep, I was under my 07 jeep plenty for upgrades and fluid changes and never saw any hint of significant rust. I've never given an undercoating any serious thoughts, but know you have gotten my brain rolling. Just to let you know the drive shafts will get a layer of surface rust on them, but it is really nothing to worry about.
Ok, that my opinion...I could be wrong.