I have some work to do, so it will be a few hours before I can take a good look at this. In the meantime you could try the following.
This is just a test and you shouldn't operate you machine very long for this test.
If you have a router as your spindle, take it off to lessen the weight. Disconnect the wires of the Y stepper motor on the right of the machine, the one with just one set of wires hooked to it. If you used the terminal blocks just un-hook the motor and leave the add on wire hooked to the terminal block.
Turn on your machine and try to jog your machine on the Y axis and note the results. See if the gantry moves and if it moves in the correct direction.
I'll get back to this later today.