Thanks, Neale. I'll have another think about it. What you describe is pretty much what I'd planned on doing and then I was standing there yesterday looking at the parts and I started wondering if it was going to work. My concern in terrible ascii art is something like this:

Code:
  y axis (in home position)
        V
    ________
    /      /
   /      /  <-- The x rails are parallel but not perpendicular to the y axis
  /      /
Ah, now I've drawn it out I can see the method you describe will work. You just use the second x-axis stepper to pull the gantry into alignment.

Thanks again. I'm sure I'll have plenty of other stupid questions :-)