Joe,

I thought this explained it, http://www.mycncuk.com/threads/6565-...5217#post55217
For the first X rail I used a straight edge to mount it. For the second X rail I used a measurement from the first X rail but in the end I used the Hiwin bearings to line it up.
By moving the gantry back and forth it was easy to find the position of least resistance and the second X rail was tightened down in that position.