The stepper/ball screw/support assemblies were ready to be attached to the machine. I used some K clamps across the width of the machine to use as supports to lay the assemblies on while I worked on aligning them properly.
First, I determined the front-back positioning. Moving the gantry to one end of travel, and the ball nut to the same end of its travel, I aligned the center of the ball nut coupler with the center point between the X linear bearing blocks. Then I clamped the assembly in place on that end. Moving the gantry and ball nut to the other end of their travel, I aligned the ball nut coupler with the center of the linear bearing blocks and measured the extra travel available on the ball screw. I split this measurement in half to allow equal space on both ends. I readjusted the position accordingly on both ends and clamped in place again.
To get the vertical alignment correct, I mounted the wooden piece to the ball nut coupler that would attach to the gantry. I moved one end up to the gantry, readjusting the k-clamp to set the new height, re-clamped the assembly, and then moved the ball nut and gantry back to the other end and repeated.
With everything in place and aligned, I unclamped one end at a time, applied wood glue, and re-clamped.
I then repeated the whole process for the second X axis drive assembly on the other side of the machine. After the glue was dry and I reconfirmed the alignment was still correct, I glued the pieces in place that attach the ball nut couplers to the gantry.