Happy to co-operate but I dont really understand what you mean. The Aimtrak requires no software to calibrate and this should only need to be done when the guns are first installed.
The OP's goal is to recalibrate the gun each time a game is started because people of varying heights and shooting styles will be firing from different positions.
Just out of curiosity, is there a way to trip the calibration process via command line?
It would be a simple matter to make an autohotkey script that would throw up a splash screen with targets on it, then exit upon a key press.