I finally received the PCBs from OSH Park and they worked great right out of the gate. I tried round machine pins, instead of the usual break away headers, and found they felt much better when plugging the backpack in. Pictures and more info after the break.
A New Design
I also created a new design that has LEDs for the MOSI and MISO lines. These will show programming status and double as LEDs that can be used for impromptu debugging on PB3 and PB4. I should be getting the new PCBs next week.