I am also putting in a 5.2 and Dana 44's. See my build thread in my signature. My engine is really a 1970 318 with magnum heads, and a stroker kit which increases the size to 6.4L, or 390 cubic inches.
Did you get the Dana 44 axles out of the Wagoneer?
My YJ/CJ V8 Magnum Build: http://jeepforum.com/forum/f22/magnum-force-mopar-mans-build-1412306/