Screw mapping is designed to map errors in accumulated movement in the same direction as the screw itself. There is no association made between errors on the Y axis screw and the other two axis.
Some kind of complex transformation equations could likely be created to apply to your program to correct it when run on the machine. But, that sounds like more of a nightmare than just fixing the alignment of the axis.
Pick the least adjustable axis on your machine to serve as a baseline. Square the other axis to it. Probably one method to do this is write a program to drill holes at the corners of a right triangle, insert pins, measure the seperation of the pins at the hypotenuse. One favoured combination of sides for such a right triangle is 3,4,5 units, because any triangle with those specs contains a perfect right angle. So program 3" in X and 4" in Y and then measure the third side accurately with a digital caliper. Adjust one axis to try to reduce the error.
The longer the sides of the triangle you use, the more accuracy you can achieve. You can scale up the 3,4,5 triangle to 6,8,10 or 9,12,15
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)