The VCM controls are live while the scanner is is connected. BTW give the cylinder balance test..it is very interesting to see how the HPT takes over the engine. As far as the fans, you would have to keep the scanner connected and the fans commanded on so they won't shut off.
A CASE learn, is something you would only do if you changed out the PCM, and a few other items. Most don't mess with it unless a code is thrown referencing the Crank Position Sensor. If you atttempt a CASE learn and one isn't required it won't allow you to complete the process.
I've never created the boost parameter so someone else will have to help you with that.