The base can be a piece of plywood, or a tabletop that you're willing to drill holes in. The CAD model shows a 24 inch square piece of plywood that is 0.5 inches thick.
The base needs holes for the arm and 2 printed circuit boards. The PCBs only really need 2 holes, but the arm should have all 4. Use a 4.5mm drill bit. You can print this PDF to use as a template for the holes: BASE-1TO1-1.0.pdf
Use M4x25 screws with nylon lock nuts and oversize washers to mount the riser to the base. The oversize washers will prevent the screws from digging into the plywood.
Add M2.5 standoffs to the PCB brackets using nuts on the bottom of the brackets.
Use M4x25 screws and nuts with oversize washers.
Use 4 M2.5 screws to mount the Arduino Mega (or clone) to its bracket. Do the same for the DC motor driver.
Push the main PCBA into the Arduino Mega (A4-PCBA-1.0).