YIKES!  You say "unusual" damage, the drive faces of these gears should
be as smooth as mirrors.  Any small nicks or dings will cause
considerable metal-metal contact and overheating, especially at highway
speed.  The hypoid gears make a VERY sliding sort of "contact", and if
there are mars on the surface, that will cause rubbing of the metal.
They will eventually smooth off again, I suppose.  if you do try to
continue using this differential, I would see about getting magnetic
drain plugs for it, or making them if you have to (not very hard).
Then, I would go out for a short drive, drain the diff and refill.
If you want, you could take the oil and run it through a fine filter
and reuse it.  A large filter paper in a funnel left to drain overnight
should get the metal out.  The full diff contents might take several
separate funnels to run through in one day, though, as that stuff is
awfully thick even without foreign matter.

Otherwise, I'd keep draining and refilling it at gradually longer
intervals until you don't see any metal on the magnets anymore.
Of course, you HAVE to find out what bolt that retainer flap was
SUPPOSED to hold in place, and re-do that section.

Oh, hell, I didn't even MENTION bearings.  This kind of crud must be
even harder on the bearings than the gear teeth!  I think the main
tapered roller bearings may SOUND fine right now, but they are going to
fail for sure after this abuse.

Jon

I decided to take pictures as I go along. See

http://igor.chudov.com/projects/Automotive/Drivetrain-Noise-In-Dodge-RAM-1500-Pickup/

Some findings as I opened up the differential.

1. It is full of gear oil. (means my oil change 2 years ago was successful)

2. On the bottom there is some amount of of, like, 100 grit metal
dust, settled down.

3. There was one foreign object on the bottom, see

  http://tinyurl.com/zr8zg

4. The gears and such, do not seem to have any unusual damage.

i