I see what you're saying now, it just took me a second explanation to understand.
You are choosing when you want the intake to be closed, which determines the compression and the effective size of the engine (or at least effective displacement). Do you have a button inside the car to tell the system what you want or is it still automated?
So, since it is from a Prius, that means you have the FXE? How do you get around the hybrid battery stuff? Is that why you need a different ECU?
I've gotta find me a place that sells these! For $200, experimentation is very possible!