Gawd-dang, cleaning that car by your description makes it a project car by itself.
I picked up that Auto Febreze (it's in a gray bottle) from the discount rack at Target a while back. Works nicely for occasional odor reduction, but don't over-do it. Remove everything that isn't bolted down, and vacuum out everything. Wash and wipe-down everything, and underneath the seats might be all sorts of ungodly treasures. Make sure the carpeting is not entirely soaked with water, otherwise the water seeps down underneath the carpet, thus mold and more odors start to form. Make sure the carpet is as dry as can be before putting the mats over it. Hose out the floor mats with soap and water. Scrub them with a bristle brush (the trick to hide stains is to use a "combing" motion in one direction throughout the entire mat). Leave them out to dry for a few days, although use a wet-dry vacuum to get most of the water out first.
My old Corolla was a smoker's car, and I just washed the interior frequently for about a week, during the driest time of year (that's when I acquired it). Blowing some compressed air takes out all the hidden crap in the car. Don't forget the headliner, it's usually the smokiest part of the car (since smoke rises). Some things like the old car mats, are best replaced with new ones; Nissan's set might be a bit steep, but Wal-Mart and others have their own varieties.
It's also an Xterra, it's supposed to have that macho-anti-clean look. Although dirt and use is one thing, food wrappers and bags are still unacceptable; although eating kids do a number on the back seat. How many legacy Goldfish crackers will I find today?
I would also get that rear-window replaced as soon as possible; thieves tend to think that once a car is stricken, the owner will return to leaving all sorts of valuable goodies in the car. Even if it was not damaged by a break-in, that plastic bag gives easy entry to thieves who might not think that tearing a plastic bag is as much of a crime as smashing a window. People who might not normally commit crimes will steal things form an unlocked door, but they won't necessarily cross the psychological threshold of breaking-and-entering (the destruction of property).