First, 3D print the control box top and bottom as well as the indicator box front and back. While these are printing, you can start on assembling the circuit board as described in the next step.

Follow the Circuit Schematic and solder the circuit together as shown in the pictures. The Components section below details the required components and specifications of which of each electronic component to get, as well as the hardware used while creating the case. The resulting piece of circuit board should fit with some extra space into the control box bottom. Note: only solder the wires for the joystick, power LED, capacitors, switch, and cable (to the indicator lights), as we will be attaching those after the top of the control box is assembled.

Next, push the joystick into the top of the case (you will probably need to remove the switch cap for this, and may need to break off any plastic pieces that stop it from sitting flush on the case). The pins should stick through the bottom just enough to solder, and the four metal clips should easily bend to tightly attach the joystick to the case. After this, push the LED in (you can use some glue or epoxy if it doesn't fit snugly) and attach the switch. Finally, solder the wires left as guided by the schematic and pictures.

Using the same technique as to insert the power indicator LED, add the 5 indicator LEDs as a first step. Next, solder on the wires and resistors (Tip: it will be a very tight fit, so be careful not to leave excess wire!). Then finally attach one end of the four-wire cable to the wires from the LEDs and resistors (there should be a common cathode to all, and three anodes attached to the groups of LEDs).

Finally, attach the other end of the four-wire cable from the indicator box through the hole in the bottom of the control box to the circuit board. Then, add the capacitors through the hole in the bottom of the control box (Note: you can use a socket as I did in the pictures or just connect them directly). Next, add some glue/double-sided tape and press all of the circuitry into the bottom of the control box. This will be another tight fit, so you will need to be careful that none of the connections break when doing this. (Tip: Test the circuit before putting it all together, or you might have to risk reopening the box and further stressing the wires)

The one remaining step is to add the screws to the indicator box and control box, and you're done!