Stock ford rear 60's suck, 30 spline small axle shafts, not much stronger than a d44.
If you are going to build it up it is fine, the housing will take a 35 spline locker and then 35 spline shafts.
For the rear for something you would find in a JY it is tough to beat a GM 14 bolt, they are easy to find in yards, detroits are cheap for them you won't need chromo axle shafts, it is easy to re-gear them since they have adjusting collars in them. Disk brake kits are pretty easy and cheap (unless you need a parking brake...) They are huge and heavy
Dana 70 out of a dodge ram or ford van is a good option too.
For the front, 78-79 ford dana 60 is probably what you want. They have king pins instead of ball joints, and the driver side axle tube is pretty long it seems like it fits pretty good for full width. (and good luck finding one in a JY, it happens but not often)
Of course if you find a newer superduty with the "super 60" that is pretty sweet too, just be sure to get the matching rear axle since the superduty's have a metric 8 lug pattern.
This is just to get you thinking... I could go on for pages but I won't.
Nathan
99 xj, one ton's dual cases, 37's
build thread
http://rme4x4.com/showthread.php?t=83436