As to figuring drops and trajectories, etc, I believe the sight height that needs to be used in computations, is the height of the front sight above the centre of the bore (projectiles axis), just as that is used in figuring drops and trajectories in modern guns with iron sights and scopes. This makes a considerable difference in the actual trajectories produced by the ball.
To figure the actual sight heigh above the bore's centre - merely divide your muzzle diameter by 2 (assuming the bore is in the middle), and add the front sight height to the product.
The rear sight height is not important in equations, as every zero sighting hinges on the height of the front sight above the centre of the bore - it stays the same no matter the zero range.