I have my primary objectives of switches and lights done. And it works!

There are two errors which I discovered. One pairs of pins going to A4 and A5 are swapped in the footprint artwork for the dual row connector. So those LEDs are swapped. Not a big deal - I can hack the software to get them to display correctly. The second is I have my STOP/RUN switch backwards. Again, I can swap it in software. If I do another board spin, I will fix those errors and the via solder mask problem.

I have kill-the-bit up and running and it looks like it's working ok. I haven't finished checking every LED and switch, so there may be more hidden errors. Next is get the microSD card reader up and running so I can have disks!