I had a similar issue withe my 04 530i though it is a six speed. I had a stumble at around 3 to 4 thousand rpm you could see the rpm hand stumble and feel it in the seat of your pants. ddealer was stumped they kept the car for weeks on end finally there fix was a ecm flash, had to remove the ecm ship it to new Jersey engineering to reflash. it seemed to work for a month or so but came back. I just finally figured out my issue was my alkternator regulator it was overcharging and not only causing the hesitation,but on cold mornings it would flicker lights and flicker off the radio for the first two to three minutes of start up also would get every conceivable error until restart. I replaced the alternator on a whim and it fixed all my issues. I tried multimeter's on the battery on startup and also did the hidden voltage dash thing and of course it always worked when I did that so I took the chance and chanced right. cat even seems quicker now like it did when I first brought it.