Hey,
I have had my CAI for over two years with no issues at all. The position the intake puts the MAF can affect the way the car runs, but would not cause what I saw in the video. One thing I noticed is that it only happened after the fan kicked in.
Has the intake manifold been taken off? I am wondering if there is a vacuum leak, or a problem with the VTCS.
Putting the stock intake back in is only going to help eliminate variables in finding the true problem. After seeing the video, I am highly doubtful that the wires/MAF are the issue. If there was a problem with though items, it would happen all the time. I am wondering about the vacuum lines and solenoid near the throttle body that need to be strapped to the intake. I have heard that they can be damaged when people try to put on an intake.
Here is some picture of my X3 ebay intake (injen style)
Yes that is an AEM bypass