I had similar issue a few months after replacing the intake elbow and it turned out to be some of the related vacuum hoses and a cracked vacuum fitting. As the engine transitioned off cold start, it would stumble. Once fully warmed up, it ran better, but still with a bit of a rough idle. I agree with crystalworks on the coils too. My two replacements came at 124,000 miles on the e53, but my wife's e46 had three go bad at 100,000 miles.

2002 X5 3.0 290,000 miles
2004 325i 123,000 miles