Well, obviously you have a front end issue as well, if removing the front shaft eased up the steering.
Find out the front hubs aren't locked by jacking up the front end and turning each wheel and see if the diff pinion/front shaft turns.
Gentle turning as well as sudden jerking turning of the wheel might help diagnosing possible intermittent lockup of a bad auto hub.
Have you checked the rear uni joint for any play? Make sure a wheel is chocked up, not in gear and the hand brake is not on when you do that. Jack up the rear wheels and try to twist and push and pull the uni joint. Jacking up the rear wheels may not be important, but I reckon it can help with the feeling.
Seeing little bit of metal filing on the diff bung is not necessarily a bad thing.
Another thing came to my mind is that make sure the diff breather hose(both front and back) are not blocked. When the diff filler bung is out, blowing into the breather hose is a good way to find whether it's blocked or not. Blocked diff breathers can cause all kind of dramas, including oil seal failure and leaking diff oil and leaving it dry eventually. The blockage could be either inside the rubber hose or the diff breather hole or both.
Also make sure you use the proper LSD oil for the diff. Rear diff is definitely LSD. Front can be either LSD or open, depending on the history of the vehicle.
Considering what you've posted so far, I'm bit suspicious of the transfer and the gearbox, but you need to rule out the rear diff & uni joint first, 'cos AFAIK, they are a pretty common cause of drive train noise. Should I say rear uni joint(s)? See if the uni joints are in good overall look or whether they look like covered in crap. They need greasing as well, but that's out of question if one of them is already worn out.
BTW, uni joints are really happy when you mark them before removing and put back in exactly the same way it was before.
They can produce noises that wasnt there before when you do otherwise.
So, remove front and test drive(you've already done that)
Remove rear and test drive with front drive.