[4-Door Flunky]

Hi, Corey-
I'm not an expert, but I have read a lot of information about things that go wrong with these cars, and CV joints aren't one of them.
My 1985 535i clunks because the Guibo and/or the driveshaft support bearing are worn.
The guibo is a rubber flex-coupling between the back of the transmission and the driveshaft. It gets worn, creating a little bit of slack in the driveshaft and you hear a 'bump!' noise any time there's a transition.
Same thing with the driveshaft support bearing.
Are you hearing this noise when you use the brakes?
I hear mine upon take off. I hear it especially if I'm slowing down for a light and then give it some gas to speed up. If your car makes the noise under the same conditions, it's the guibo and/or the driveshaft support (sometimes called a center bearing).
You can get a Guibo for about a hundred bucks, and the driveshaft support is regularly on eBay for about $30. Replace both while you have the driveshaft out.
Failure to fix these things will eventually thrash the driveshaft, which costs about a thousand bucks.
Let me know if it's only making the noise when you use the brakes. That would be a different story.
Flunky