Rear diff mount:
See fig 7 in this link: Differential DYI instructions - E46Fanatics
Also see item 9 in this link: RealOEM.COM * BMW E46 328i REAR AXLE CARRIER
The bushing itself is about $30. Labor is the killer. Diff must be removed, then old bushing pressed out, new one pressed in and diff installed. I've heard of quotes between $300 and $800. With all the other work you have had done, I'm surprised no one mentioned the rear diff mount.
This link shows a bad bushing (it also shows subframe damage....not pretty):
Whats bad about it is the rubber part is torn. The hole is supposed to be oval shapped. Another one bites the dust: rear subframe damage - E46Fanatics
Note: If you are unlucky enuf to have a torn or damaged subframe, make sure you go here: Girard Gibbs LLP - Investigation of BMW
I've done a lot of reading on this subject in the last couple of weeks because I have the same problem and am determined to find the cause. All other threads that bring up this issue just die out with no resolution. Some say "its normal", I dont buy it. Some say "all high mileage cars have funny noises, live with it". True, but they can be fixed. I havent heard of a for sure fix for this problem.
The one component that has not been mentioned in all the threads I have read is the differential itself. Diff bushings, suspension bushings, subframe bushings, trans output flange....all these things have been mentioned. In some cases replacing the rear diff bushing helped, in other cases it did not. The same is true for the other parts just mentioned. But I have not read one post that said the repair eliminated the noise completely and permanently (permanently=until the offending part wears out again). Again, no one has mentioned the differential itself.
I'd like to hear from someone that has replaced their diff in an attmept to fix this problem.