Since the bolt holes in the base are bigger than an M3 bolt, the base can tilt a bit. By tightening the face plate holding the bearing to the face, the Y rod itself forces the base to be perfectly vertical. Then you can tighten the bolts holding the base to the solidoodle. After that you can loosen the faceplate so any stress caused by cranking down the base is relieved and re-tighten and the theory is the rod will now be perfectly supported. At this point, you can tighten down the Y motor and it shouldn't cause the rod to deflect as much.