I had exactly the same problem in my '08 (no mods)-- fuel pump and injectors replaced, then the slightly rough idle. I took it to the dealership and the Service Mgr sat with me in it for about 5 minutes and said that he felt it. I have 42k miles so he offered to clean carbon buildup. They took the car for 4 days, said they found "some, but not much" buildup, returned to me. It was okay for about 2 weeks but I'm starting to notice it again. Almost out of warranty, and starting to worry. Also, now that it's warm up and I'm driving with the windows down I'm noticing a more distinct rumble when downshifting to slow down-- like you'd hear on an old car-- wondering if this is related? Oh, and to top it off I hear what I think is the waste gate rattle coming on!
LOVE LOVE LOVE this car, but honestly, will this ever end?! I keep telling myself that at some point I will get through all of the "typical" 335i problems and then the car will be good, but I'm starting to lose hope....