The 'clicking' sound is completely normal for the M54 engine after you've run it hard. I learned about this from the BMW guys after my first auto-x myself. After a few hard runs, just open the hood and keep the engine running, let it idle for a while and the engine will be fine. On the drive home, keep the revs low and just cruise and the noise will be gone before you hit your driveway.
I wish I could give you a better / more technical description of what's going on in there, but I'm not an engine mechanic. That said, I have been assured by a mechanic and other M54 owners its completely normal.
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