I just finished breaking it in. Got almost 2500 km on there. I noticed that the rough idle went away when I pressed the clutch in and put it in reverse (without disengaging the clutch). I then kept the clutch depressed and put it into neutral, and the rough idle stopped.
Also, the clunk only happens sometimes in reverse. I think I'm going to take the car in to BMW to look at it. At least there'll be a record of it if something goes wrong in the future.
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