The sight radius is the distance between the rear and the front sights. I measure between the rear surface of the rear sight to the rear of the front sight.
The caliber has nothing to do with the calculation except that it will affect the muzzle velocity given the same powder charge. You need to use the load tables to determine the approximate muzzle velocity of your load. Given the extreme mass of the earth, the mass of a falling object is irrelevant with regard to its effect on gravitational attraction. Therefore, the acceleration due to gravity is considered a constant for all falling objects on the earth. Remember the experiment with the feather and the canon ball. They both fall at the same rate; ie... the acceleration due to gravity of 32 f/s^2 or 9.81 m/s^2. Now given that force=mass x acceleration, the force (the weight) exerted on each object by gravity is very different. In other words, the canon ball will make a bigger dent in the ground when it hits than the feather.
I hope that helps explain things better. The calculations I use are pretty simple physics and trig calculations. I do make simplifying assumptions such as ignoring wind resistance and that fact that the bullet travels in an arc as opposed to a straight line. The purpose is to get the front sight height very close to the final sighted in height without making it too short. I want to be close to the black on the first shot as opposed to completely outside the target area completely.
In the past, I have just made these calculation on paper went I made the front sight. This time, I decided to make a spreadsheet to do the calculations and uploaded the spreadsheet to my iPhone to run under the Spreadsheet app. Using these calculations, it usually takes me five shots to get solidly in the black which is as much as I do on any rifle I sell. I always sights with the same load; ball .005" under bore, .020" ticking patch pre-lubed with a dried Ballistol/water mix(1:7), and a charge 1.5 times the bore. I use FFFG for 45 caliber and under, and FFG for 50 caliber and over.