When I researched this, I concluded that all the differentials are a direct swap physically. That is to say you can bolt any differential into any E53.
The difference is in the halfshafts and output shafts. There are subtle differences in the bolt circle on the output shafts that make the halfshafts not all interchange. You cannot tell by eyeballing because the difference is a few millimeters. But when you go to bolt up, the halfshaft will not seat all 6 bolts.
What I ended up doing was using halfshafts with part numbers that matched the differential I swapped in, and I used the output shafts that came with the differential I was swapping in, not the one I already had.
I believe not all outputs will seat in all differentials. Some outputs are a bit more robust, if I recall correctly, and have a slightly bigger OD of the splined portion of the flange. I might have pictures to show this, but I would have to see if they are backed up because my phone SD card failed.
My suggestion is to use RealOEM to match up diff/output/halfshaft and make triple sure it will physically all seat and bolt up before you have car down to bare subframes.
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2001 E53 3.0 5pd
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