I have owned both a 2000 XJ 4x4 and now an 87 grand wagoneer! I do miss the xj but not enough to sell my FSJ. With my xj I got 17 mpg everywhere I went, highway or city, now I get about 11 city and just over 13 highway in the GW. I think I can do better. My GW is reliable but I don't go far without a tool bag. I love to upgrade, always messing with something. Most XJs I have seen that are tricked out are not really appealing to me (it's personal, I know). I never turned heads in it either. The FSJ is absolutely my favorite so far but it is not my daily driver, it is my baby!
If you are planning a swap either way I would do an FSJ with a 5.3 swap. The guys who have done this get 15 mpg, have a reliable mpfi rig, tons of power and a crazy cool engine bay. If I was gonna go through that trouble I would get a 08 or later 5.3 with active fuel management and hit every bit as good mpg as my xj got with something way cooler. The older wagons are harder to find parts for, you will be scouring the yards and internet for many items. I hear AMC FSJs are a bit easier than previous manufactures but it doesn't seem like it.
Grand Wagoneer - rebuilt 360, 727, Dana 44's, EDL 1406 & 2131, HEI cap & TFI coil