having done it myself in my CJ, I would HIGHLY recommend building a deck over the entire rear end of the jeep. run a two by four length wise down either fender, and then another on each end and perhaps a two by two across the mid section. Use some 5/8ths OSB (or if you can use aluminum) and cover that with some shag carpet. With that setup you will have a very large amount of space under the deck that no one can get into without effort, you have a great place for your dog (which you can put in some I-bolts to hook the leash/belt to) and you have a lot of storage under the back deck. For jeeps, especially a cj, the low COG is an important factor. If you end up still feeling the need to install a rack on top, you will have less up there, and you can keep all of the really heavy stuff inside on the floor.
If you go XJ engine, then get yourself an auto tranny as well. This will change a lot for you with the drive shafts and such, but wow it sure is nice to have that engine and tranny set up. (would love to do it to my cj, but the wires scare me too much.) If you decide that you want more tire space, seriously give consideration to tub fenders. They open up your wheel wells a lot, and still keep the COG low. Gen-right has a really nice "high-line" set up, that if I ever get an unlimited I am going with for sure! You can run 37's on stock suspension! This is not to mention the fact that the entire fender set up costs less than any lift kit would cost to aford the same tire size.
You have a nice setup there, good luck on your trip.
by the by, yeah, all of the Posts are going to charging you five bucks just to use the bay for half an hour, and all of that. Used to work on my car back at Ft. Belvour for free. Sure miss those days.
Brian