Another way to do it:
First, make sure your mill's column is perfectly plumb and the machine is securely fixed to the floor or bench (this doesn't work well with machines on wheels). Next, securely attach a small laser module to the side of the mill's head, the smaller the laser's dot the better. Aim the beam at a far wall, 10'-20' away works well. Mark a plumb, vertical line on the wall at the dot. Then even time you move the head simply align the laser dot to the line on the wall, any error is magnified, if the machine and vertical line are true, you can easily realign the head to within a couple of thousandths.