EDIT: Cleaning the MAF solved this issue for me. Someone else ran across my description of this problem in a thread on bimmerforums and saw that cleaning the MAF had fixed it for me. After cleaning his own didn't work, he PM'd me and bought my old MAF (that I had cleaned and kept after I upgraded to the 3.5" MAF). After installing the one he bought from me his problem went away.
That's 2 examples of this problem solved by a MAF so anyone else coming across this should start there.
