I am confused, which may not help you much, but D2 on the 5V ALWSR build in the online manual parts list is a 1N5333B, but the schematic has a LED, and the component overlay has a LED. I think the online manual 5V build schematic and component overlay are a bit out of date?
I believe a zener needs to be the opposite way round to a LED.
From the online manual component overlay the LED is shown anode at the top, cathode at the bottom.
From your photo, although the PCB is not the same, it is shown in the same orientation, and has the zener cathode at the top, anode at the bottom.
So you would need to add the LED in the opposite orientation to the zener, as shown in the online manual I believe.