Alright, that was annoying. Here's the full board:

Despite getting the shift register/LED driver thingy right, this was a farily annoying board to route. For exhibit one, I present something from the Sparkfun Eagle library:

Genius.

Now that this is done, I'm going to run the DCR, sleep on it, check it again in the morning, and send it off to OSHPark. It's ~$45 without a stencil, so not too bad. The total BOM cost of this clock is looking like it's going to end up somewhere around $200. Oh well.