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Try moving the two X axis sliders oppositely but with the steppers locked/driven. You will see that they stay at the squareness that they “locked into”. If you start with the axes perpendicular then then will stay that way until the steppers are disabled. This remix is an attempt to make it easier to start out in square http://www.thingiverse.com/thing:918871. I have never tried it but let us know if it helps.
I did need to do some light sanding to remove some excess plastic extrusion on the X and Y slider/clamps which caused a bias in one direction/angle of both sides of both X and Y. I wrapped some very fine sandpaper around a dowel and it helped to tweak the X and Y to be square with the side rails.