Hi Philip,
This should not be that hard to resolve.
With the CNC powered off. Disconnect the two Y axis cables and manually move both the left and right sides to get both sides touching the end stop. Then reconnect the cables and power on. Using the joy stick or the software positioning controls, jog the y away from the end a few inches and home the CNC.
When it homes it should both touch at the same time.
This is the same processes that you may have used when you installed your CNC
I hope that helps.
Mike