Solder jumper wires to all eight of the outer pins on each rotary switch, and a normal wire to the central (ground) pin.

Solder wires to the toggle switches, one each to middle and one side pin.

For each LED, solder a jumper wire to the LED anode pin, and a 330 ohm resistor to the cathode pin; then a wire to the resistor.

Solder a jumper wire to each BNC signal pin (central pin), and a normal wire to each BNC ground (side pin).

If using dimming version: solder a jumper wire to the central pin on each potentiometer, and a normal wire to pin 1 (for +5V) and a normal wire to pin 3 (for ground)

Jumper wires make it easy to connect to the Arduino I/O pins, but there aren't sufficient ground pins, so you need to use normal wires, then solder those together.

Any exposed regions can be shielded with heat-shrink tubing if there is any concern of movement/contacting other bits.

Plug the collated ground wires into an Arduino Ground pin, and the collated +5V wires into a +5V pin (if using a Due, use the +3.3V pin or you will damage the microcontroller) and plug the other jumper wires into the correct I/O pins:

Toggle switches – 2, 3, 4, 5

Pilot LED’s 6, 7, 8, 9

TTL outputs – 10, 11, 12, 13

Rotary switch 1 (ontimes) – 39, 41, 43, 45, 47, 49, 51, 53

Rotary switch 2 (frequency) – 38, 40, 42, 44, 46, 48, 50, 52

Potentiometers (if being used) – A0, A1, A2, A3

Download the .ino file and upload the code to your Arduino Mega. If using the dimming version, I recommend using an Arduino Due (it has the same pin architecture as the Mega, but faster PWM).

Drill holes in the case for each component, keeping in mind that there is not much room in the case, so place the hole appropriately to allow room for soldered wires etc. around the Arduino pins. You will also need to drill holes in the base aligned to holes in the Arduino to bolt it in place with the M3 screws and spacers. Push the components through and bolt in place using provided nuts (the LED will need to be glued in place; I used superglue).

Depending on which case you have purchased, it might need to be glued shut. If so, be sure to test the TTL driver works as needed before sealing shut. You can still access the Arduino Programming port after the case is sealed, so the program can be modified after assembly; you just want to make sure everything is properly connected. 

Push the potentiometer knobs onto the rotary switches (and potentiometers if using the dimming version) and apply markers (I used cut up labels) to identify switch positions - this is easily done by connecting the TTL output to an oscilloscope or LED and noting which positions produce each set firing pattern.