Brian,

Sorry I can't help with your original problem. I am kicking myself for not putting an icsp port on my boards! Same problem. Good luck. In future designs I am going to put a header that will allow me to connect in with a little "middle man" board that has the 10k resistor and diode (the LL4148 works great for this) on board. Then If I have issues I only have to connect a single header.

You don't suppose you could chare the interface code to the huge SPI Flash memory that you are using? I would love to use these in an upcoming project.