Step 4: Y Axis
As with the Y Axis carriage, putting the Y axis up on some small spacers seems to help the initial setup, and then you can go around and adjust them one by one. For us, the space was about 1/2", and we found that two post-it pads was about right. Make sure the Y Axis 1x3 t-slot is square in the frame as you make your adjustments.
We were avoiding making custom brackets, but clearly, this would be a good place for them if you are so inclined.