On the M54 it could be that the brake booster/grommet is leaking. Spark plugs are critical with individual coils because they produce a lot less voltage than old school coils, also going to an iridium or ruthenium plug with wire electrodes can be a big improvement in igniting fuel mixture. My E70 had a stumble (sometimes stall) after starting and it turned out to be carbon build up from the previous owner not using premium fuel, a few tank fulls of premium was the answer to that.

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1988 325is (purchased new) sold
2004 X5 3.0 2005 X3 2.5
2008 X5 3.0 (new to me)