X2 on talking you out of spare on the roof. Been there and done that, what a PITA to get it up there, and even get it down. I had one on my old Samurai as well, lower, easier, but still a pain, especially by yourself.
I built a front hitch (from an old class III receiver hitch from a Ford) welded it between the frame rails, then built my own tire carrier and hung the spare on the front. The wheels I have are pretty open, and must flow a lot of air to the radiator, as I've paid close attention and never noticed increased water temps, even while towing.
A roof rack is great though, perfect for less used things, easy up, folding camp table, chairs, firewood, skis, snow shoes, small bbq. I have a Yakama rocket box that I sometimes put up there, to keep things out of the elements.
1995 E350 7.3 Diesel, 4x4 high roof camper, UJOR 4" lift