if you are getting the same diagonal measurements, there is only the center gantry left.
I know it sucks but you need to rebuild it. In the instructions it says to check for square before final assembly. Take the center off with the tubes and the z axis, take all the long bolts out of the assembly and put it back together. check for correct (light) tension and square at each step.
It does suck but it pays off to get this right. Then before you start each cut verify it is equidistant from the corner blocks. The more square your assembly the easier that is.