This is really funny, because I'm having the same issue with the rattling.
I just got my turbo replaced apparently and I'm still getting rattle noise on cold start, pretty much the same as it was before the turbo replacement. I also think there are rattling noises between the 3000-4500rpm range, but only when driving and not stationary revving.
I'm wanting to go back to my dealer and have them look at it again, but they seem to be a little incompetent or have little knowledge of the rattle issue. In fact it was me who suggested they look at the wastegate.
Not sure if this is similar to the N54, but I think I'm going to ask about the vacuum pump..