I have an Instructable for calibrating all axis and the extruder without having to print a calibration cube over and over. This a mechanical calibration of your printer, this is ideal just after setup or changing components on your printer. This may also help if you are having issues with your prints.
You can find the Instructable here.
You will need calipers that have a depth rod/blade; digital will work the best for the math.
I hope this helps.
I have included my 25x25x25 calibration cube to test your new settings.