I've decided that this is the project where I dive head first into surface mount.  To that end I've decided to see just how small I can make the board.  At the moment it's .65" x 1.55".  The 328 is TQFP32, the RTC is SO8, and the resistors and caps are all 805.  To save space for the ISP headers I'm going to try this board edge technique. (As I write this I wonder why I still have a through-hole crystal on the board?)

I'm also going to try panelizing for the first time and get another design printed at the same time to make the most of the 5x5 space I have to work with (a TQFP32 AT90USB162 breakout).

As for the software, it's mostly working on my breadboard.  I've got it driving the WS2811 strip, reading my Apple remote, and working with the RTC over i2c and using the 1Hz clock output -- all using the internal 8MHz oscillator.  The code for driving the ws2811 at 8MHz was found here.