Did you ever solve the rattle? I'm doing a full rebuild on mine and it also has the rattle currently. I have noticed that after it stops closing if I crank it shut with the allen driver it will slide the glass up further and lock it in place. I assume this is due to some broken plastic in there or something of that nature that is causing looseness. Just curious to see if you ever found the problem.

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2004 e53 m54 with 6spd manual