The output shaft is different between the P and J type ODs; the green book doesn't mention any changes otherwise.
The bell housings are all aluminum; it's the trans case that may be cast iron or aluminum.
"Sets"?; if you mean are parts available, the answer is yes. All at the $tealer; FCP has synchros, which, other than readily available bearings, is all you'll likely need for a rebuild.
I guess if you bang shifts like a 15-year-old, the iron case would be stronger; I have ~208K miles on my Al cased M46 and I still do track days with it, no problem.
Try Redline MTL for shifting troubles.