Just re-read your use and build goals and have to agree with other posters that the roof mounted spare is not a great idea.
Unless you plan to sleep in the rig, think seriously about leaving the tire in the stock location. A 31" tire/wheel will fit. If not, run with the rear seat down or removed. Finally, mount the tire to the floor itself and build a flat floor above it for storage.
If something needs to go on the roof, it should be light duty stuff like tents, Therm-a-rests, folding chairs, etc.
Heavy stuff and things that suffer in weather, should be inside. I know you're in AZ but keeping your Hi-Lift clean and dry is a surefire way to make sure it works when you need it.
My rig weighs in at 4560 pounds and nothing is stowed above the window line and it works really well. Weight balance is about 53/47 and it handles nicely.
Finally, the XJ already suffers from lackluster fuel economy. Add the roof rack and it has, in my prior use, about an 8-10% negative effect.