I've given squaring up the y to the x axis a little thought as well. I've seen Jonathan mention using dowel pins and long calipers but I was thinking a good first pass would be to fit a pen in place of the router and get the machine to draw a large square or rectangle. Measured corner to corner the two measurements should be the same if the gantry is square. This is how I square pieces up when working wood, it's pretty easy to get a good level of accuracy and it costs nothing.