Cannot cut a square

Are you using an X-Controller(or similar) to run both y-motors individually or are they tied together as setup in the stock configuration? Have you checked wiring and possibly adjusted the voltage to the motors?

On the physical side, Did you check the diagonals of the assembly to check for squareness? Another test you could do is to use two equal blocks and space the gantry from the front and then run a test and then double check with the blocks to see if it torqued during the carve.