Have a friend drive your car and ask them to tap the brakes. Do the wheels move back a lot? That's a typical FCAB failure.
Try driving up a driveway at an angle. Does one side make the sound more than another?
I had a hell of a time finding a bad ball joint in my e39 m5. The knocking sound you described is identical, however. It was the tie rod ball joints and they only knocked when hot.
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