D2 is in the correct orientation as you can see from this picture.
Thank you for humoring me. Beautiful pictures, by the way. Sorry I couldn't help, but Adafruit support is awesome and they'll figure it out.
I have one last suggestion, but it's risky and only worth trying if Adafruit support recommends it. That being said, I just did it (without hesitation) on my clock, and my clock still works great.
Power the clock, press the MENU button, find a short segment of wire, and (with a steady hand) temporarily short pin 1 and pin 3 on Q3. (The pins closest to the edge of the board and the pin furthest from the edge of the board. Be careful not to touch the center pin.) When you press the MENU button you should hear a "tick" from the piezo. While shorting Q3, the tube should light. After the test, touch the fuse to make sure it isn't hot. If the tube lights and the fuse isn't hot, I would suspect that Q3 is bad and unable to sufficiently amplify the signal from the microcontroller. If the fuse is hot, I'd suspect a high resistance short somewhere along the route from Q3 to R3 to VBIAS. If the tube doesn't light, look at the filaments carefully to see if they dimly glow red.