What I'm saying about the PCM is is if it truly is from a 2007, it will not run in a 2001.

How many connectors does it have on it? Two or three? If two, its from a 1997-2003 car. If three, its from a 2004+ vehicle.

As I said, the vehicle cannot run with a 2007 PCM unless overkill tuned it, which he only just started doing in the past couple months.

so when the engines running the little black section of the valve doesnt go up?

If yes, its fine.

If no, disconnect the lower vacuum line on the BBV actuator that goes to the BBV solenoid. Does it go up then?

If yes, the BBV solenoid is bad. If no, the BBV actuator is bad OR you have a bad enough vacuum leak that there isn't enough vacuum to open the BBV actuator. You'd have to check that with a vacuum guage or a scan tool that can read live data. IIRC, around 10-12 in Hg is required to open the BBV actuator.