Once I was satisfied that my belts were properly tightened, and after chasing belt calibration for months (some areas of machine were great, other’s got worse, some sizes were great, some larger or smaller got worse, etc.), I finally got smart and mapped out the entire cutting area (S3, using a set of calibrated Gauge Blocks) and determined that the BELTS and PULLEYS vary in their timing. Some areas of the belt (inch to inch) are long (meaning 1.000" measure 1.004) while other areas were small (e.g. 1.000" = 0.998").
This confirmed my hypostasis that adjusting the steps per revolution was fruitless, and at that point I stopped chasing my tail. As Will said above, if I am doing something extra precise (Bearing surfaces or holes) I cut the feature under (or over) size and then adjust the program (AND Shape) to cut what I need. Using this method I have cut bearing bores to within 0.0002" (and in a few large holes, they are round too by programming the machine to cut an ellipses, since the Y error was a little more than the Y Axis).
Let me know if I didn’t make myself perfectly clear, or if you have any questions.