After the box was assembled, the linear drive system was installed. In order to do that, we first test fit the 12mm and 8mm shafts. Since the design is not optimized for stock shaft sizing, we had to machine down each one to fit the precise length required. Luckily, fellow Fab Academy student, Ted and I have a machine shop at work.
The process was done with an industrial lathe. After measuring and marking each shaft the rods were cut and deburred. Special care was taken with the Z-axis threaded rod. For it to work properly, it needs to be able to rotate on both ends. At the bottom of the case the shaft is fit directly to the stepper motor with a 5mm-8mm female coupling, and at the top an 8mm ID roller bearing is press fit into the case. The 3/8"-10 threaded rod was turned down on each end to 8mm diameter in order to receive the coupling and bearing.
Here are a few photos of the procedure.