After I made some changes to the first revision of the PCB I sent the design to OSHPark to get some boards made. It was only after I received the boards from the PCB maker that I became aware of a minor problem with the design.
There was nothing wrong with the wiring of the board. The problem was a mechanical issue. I had placed P1 beside the GPIO header. That resulted in the left side of the PCB extending out past the left edge of the Raspberry Pi PCB. This won't have any impact on the ability to use the board when the Pi is not in an enclosure. If the Pi is sitting in an enclosure there may not be enough clearance to allow the AVR programmer board to be plugged in to the GPIO header.
To fix the problem I moved the location of P1, and reduced the overall width of the board from 1.9" to 1.75". In the most recent PCB revisions I modified a few traces to shorten them and I added a ground plane to the bottom of the PCB.
I have added a 3D view of the latest revision of the AVR programmer board to the gallery. I also added front and back views of the second revision of the PCB as it was when I sent it out to OSHPark in March. I will write up some notes for the instructions section of this project page in the (I hope) near future.