the Y axis seems to be compressed. I have loaded the g-code for the roadrunner sample in the Mach3 program. After the code has completed it cycle the end result looks like a flattened roadrunner.

Use the calibration in the settings tab. There is a button next to the "Reset" button on the settings page called "Set Steps Per Unit". Select the axis you wish to calibrate. Then specify a measurement that you want the axis to travel. Once the axis has finished moving that distance, you will inform the real measurement that the axis has traveled. That axis will now be calibrated. Do this to all of the axes that you wish to calibrate.