Picked up a dial indicator and and found that the right side of the x-axis is .04 inches lower than the left side. I tried to adjust the x and y rails to no avail. Is there something else I should try? I guess I could pick up a fly cutter, but hope not to have that expense.
Please see: http://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine#Leveling_the_Work_Area and the preceding section.
Probably you’ll want to either drill out the hole or shim the bottom or top of one of the rails to adjust it.
For small projects you could just mill a pocket in an MDF or HDPE blank for a fixture.