Andy, by PJ do you mean the power jet or pilot jet? I'm presuming the power jet. I'll stick with PwrJ for the power jet and PJ (some use SJ, slow jet) for the pilot jet.
Anyway, the PwrJ is not controlled by the PGM and has nothing to do with the air solenoids. The PwrJ is controlled by the pressure drop caused by the velocity of the intake air. On an MC21 at say half open throttle the air speed is such that the pressure drop at the PwrJ opening sucks the fuel up high enough to bleed fuel into the air stream from the PwrJfirst hole. At WOT the air velocity is higher, so the pressure drop is greater and fuel is drawn from both PwrJ exits. There's also no 'switch off' so the higher the air speed, the more fuel is drawn, up to the maximum flow of the PwrJ fitted.
When you shut the throttle, the PwrJ don't flow.
The air solenoids and X and Y joints control air flow to the emulsion tubes. The solenoids allow extra air to flow at lower rpm to clean up the bottom end. This works closely with the PJ and needle straight diameter.
When you're on a high speed run, WOT, the fuelling is being taken care of by the MJ and the PwrJ. When you slam the throttle shut and get on the brakes to avoid that car pulling out in front of you, you're relying solely on the PJ to stop the thing from siezing up. bit of a worry eh? Now you know why good 2T oil is important!
Jetting's never easy, and takes a long time to try and explain fully.