Just a little update, since I swapped my differential, among other things. I have yet to actually drive it...the battery is dead. But everything is back together and torqued down.

1) The auto and manual 3.0 output flanges seem to vary only slightly.
A: total length is marginally different (a few MM).
B: the bolt pattern (measured from directly opposing holes) is a few MM off. The auto is slightly narrower, which means it will not bolt to a manual CV joint, and the reinforcement brackets do not swap.
C: The six oxide bolts that connect the halfshaft to the output flange are different. Autos have internal hex heads and manuals have external torx heads. Torque specs are different.

2) The manual flanges will go right into the auto diff, and my car now has one of each in it, since I had an episode with one of the new auto CV bearings puking its cage and ball bearings all over the garage floor. I got one from ECS that was supposed to be VIN matched to my car, which was really huge (length and splined diameter) and did not fit either differential.

3) The main driveshaft bolted straight up to the auto diff.

__________________
2001 E53 3.0 5pd