Runout is the issue you're trying to solve.
The glass plate thing seems overly complex. Just surface your spoilboard with a small diameter cutter. Then use something flat and parallel like a 123 block that will bridge over any scallops left by the small bit to take readings on at +/- x and +/- y. Then adjust your spindle alignment to get all the readings the same. I had to loosen bolts, tilt my spindle to the side, and shim under the bottom with some aluminum foil to get it lined up.
I built a bar to hold my dial test indicator. Just take a piece of aluminum, drill holes in either end, one to mount a 1/4" dowel pin and maybe a set screw to hold it in place, and the other one to mount your dti or dial indicator. Nothing has to be precision made on it as long as the pin that mounts in your spindle's collet is the right size so it mounts like a bit would.
CNC mill build thread: http://www.cnczone.com/forums/vertical_mill_lathe_project_log/110305-gantry_mill.html