Recently my 2007 335i Coupe with manual 6 speed has experienced several instances of power loss on acceleration. This was at relatively slow speed leaving a stop light and also at highway speeds to make a pass. The car feels like the ignition or fuel supply was cut for very short periods of time. This would happen as long as you were attempting to accelerate. The problem is not there all the time it comes and goes somewhat infrequently. I have had a new fuel pump installed (9/2008) as part of the SIB and the dealer (New Country Hartford) tells me that the engine management software was not changed as a result of the turbo lag issue that affected some owners. I would like to hear from other members if they have had a similar problem and what they may have done to resolve the problem. Thanks in advance for any feedback or advice.
My son is on his 3rd (or is it 4th) fuel pump. He had one replaced around the time you did; but just had it replaced again for long-start and hesitation similar to yours. You need to get it checked (again!)