I had a great idea today... I'm going to make the bottom 6 pins of the I/O connector match the pinout of the standard 6 pin AVR ISP connector. I should be able to use my pogo adapter to fuse and boatload the chips before installing the I/O connector that way. Of course, anyone who needs to re-load the bootloader in the field can make an adapter. Or, perhaps, they could try and cram an ISP 2x3 socket on the bottom 6 pins, but I think the end of an IDC DIP socket is wider than the pin pitch, so that probably won't work too well.
Meanwhile, I'm having trouble figuring out the best pin count to use on that plug. It looks like 2x13 (26 pin) is the best choice for the female end, but the goal is to have the other end end in an IDC male .3 or .5" DIP plug, and it looks like those come only in 24 pins, from what I can tell. I'm not sure what to do about that. If anyone has any bright ideas, I'm open to suggestions.
The other big connector should be easy - 2x7 is a fairly common size, and that's just female IDC on both ends. The other end will go to a "keyboard" board that has the 7 switches mounted on it (6 inputs to the MCP23017 and RESET).