Calibration for the vertical axis

it’s not a matter of changing one item to scale the Y and a different item to
scale the X, when you changed the distance between motors, you changed both the
X and Y location

see List of sources of error for a detailed
discussion of the problem

basically you need to carefully do the calibration (try a more accurate tape
measure possibly) or try the holey calibration method that’s available with
webcontrol (although you may want to wait a day, it seems a bug snuck in,
probably going to be fixed this weekend)

David Lang