Sounds like you have the dreaded low RPM/idle hiccup. Mine has come back very slightly after changing: plugs, pre-cat O2 sensors, cleaning both MAP sensors, intake cleaning (once when I bought it, once again a year later to see how fast it builds up), cleaning the valve cover internals and cleaning the PCV inside the valve cover, new VC gasket with sealant in the critical areas, and all new injectors. Unrelated items changed are the low pressure pump and low pressure sensor (died).
My plugs are getting long in the tooth for having a Procede and PWM meth for over 16k miles now, so I will try that again. I also have a new Dinan lightened dual-mass flywheel and clutch to go in, but I was incredibly sick over Christmas and all that has been pushed back. The only other thing I can think of is a misfire, or the DME perceives a misfire, due to a worn out springing medium in the DMFW. The very high HP N54s are having a misfire at high load/high RPM possibly due to the dual-mass flywheel, so I am speculating that the DMFW may cause issues at lower RPMs/loads, too. I have 65k miles on mine now.
The one thing that cleared up my idle and low RPM hiccups most noticeably was cleaning the MAP sensors, especially the one in the intake manifold. They get oiled/carbon fouled. Also changing the pre-cat O2 sensors significantly reduced the hiccups, too.
E92 335i/6MT Dinan Stage 3: intercooler, oil cooler, intake, flash, exhaust, LW dual-mass flywheel.
Vishnu PWM methanol custom trunk mount, Diffsonline 3-clutch Salisbury custom diff, Ohlins Road and Track coilovers, Vorshlag camber plates, much more...
E28 M5 w/ buncha stuff, R171 SLK350