Can't you sweep off of the faceplate in the Y direction and do the same thing?
As for the center of the axis, you know the center height of the rotary (6"). Probe the table surface, then add 6" to your G54 Z height. That height is supposed to be within 0.001".
Y-axis direction would be a little more complicated. If you have probing and a symmetrical fixture, you could probe the front and back as a really fat web. The control will split the distance and set it on the centerline.