I have gone through several iterations of stepper motor mounts. The last thing to be adjusted is the stepper through the z-nut on the bed. I found that it never lines up perfectly after assembly. With the small screws on the top fine adjustment is available. I first center then mount the z-nut on the bed securely. I then slide the motor mount under the z-nut mount and center, noting where the lead screw passes through. I then slide the bed up and down, adjust the screws, and keep the position of the lead screw in the same position in the bed z-nut mount. It takes awhile to gradually tighten all of the bolts while adjusting the screws maintaining position. Once completed the z axis stepper goes up and down easily with no binding.

The plastic nut under the z-nut bracket allows for better clamping of the z-nut. The half nut is in case you forget to put the full nut on during assembly. The half nut can go on after.

Required are: 3 mm screws, m6 sliding t-nuts, m6 x 12mm flange bolts, and an m6 x 14 socket head bolt. I also use the same 3mm inserts that Scott uses on the Hypercube Evolution.