Its the Crankshaft Position Sensor wire
The E90 can run without the Crankshaft Sensor, but poorly. The car goes into default limp mode. You get a Service Engine Light, and a Brake light. Along with a DSC Malfunction code. So, my problem was that the Crankshaft Sensor plug, was not plugged in!
335i Sport, Koni Adjustable, Cobb Accessport, VRSF FMIC