Daniel, I think you are correct on all counts. Same thing happened to your car as ours. Unit was run on no oil for quite a while before leak discovered+fixed, but too late, damage done.

If that was indeed a rebuilt unit then for sure, the gears would have been really tight-producing some amount of fine metal shavings.

I don't think you did anything wrong by replacing the new oil.

I got a used unit from Maryland, w/71k miles on it, no defects. I did put new synthetic in it, so should be good for next 200k+

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1995 MB E320 Wagon
2001 BMW 530i
2007 MINI Cooper S (!)