If the literal instructions are confusing try watching the YouTube movie:http://www.youtube.com/watch?v=6drMZqmyXQc Also check out the follow up instructions on Stepper Motor Control: Easy Mill Stepper Motor Controller
The Y stage is just like the X stage but turned 90 degrees. Mount two rails and a motor on the X Stage and then take another piece of flat material and a U channel and make the moving Y stage. Make the little bearing thing and a coupling nut for it too. When your done it should look like this.