These problems are in no way related to the K&N filter, or charcoal filter removal. You didn't put something back in right, either the MAF sensor, or the box is not connected to the intake tube properly. Feel all around the tube and make sure you have no gaps or air leaks. That is probably the issue. Check you MAF sensor too, make sure you didn't pinch the o-ring, and that it is in air-tight with no leaks. I would just take it out and re-install the air-box, don't panic. The filter or the removal of the charcoal filter wouldn't have this result. You have an air leak somewhere. I'd bet on it.
I have done this mod twice now. Once on my 06 325, and just recently on my 07 328 coupe. No issues.
On a side note, for whatever reason the 328 seems to have picked up more of an advantage from this mod. The sound is more noticeable then the 325, also throttle response is much quicker than the 325.