isnt the J20 rear wider than the front waggy(i guess it could be the widetrac front).... ifs so, i would just have the rear axle narrowed to match the front and have a set of alloy shafts made. Or narrow it to the correct with so that a stock set of replacement shafts will fit.
just ideas....
the pinion being off 2-4 inches should matter...happens every time you put a 8.8 in a TJ.
Seth