dfuprog, hm that sounds awfully familiar. When I started my cartridge programmer, I had used dfu on an erased avr chip, unaware that it actually needs a dfu firmware on it to work in the first place :D next mistake was that I would need to dfu erase first, then prog over dfu. That took me a while as well to figure out.

I get what you are saying.  That was one of the first questions I tried to resolve, however, there was definitely a voltage issue on the chip as well.  I think that I may have got solder somewhere it should not have been, not enough to create a dead short, but still making contact where it shouldn't have been.

I have been running fast and loose with the whole design/build process for this board, as I wanted to get something together to show proof of concept before the end of the semester, and I did manage to 'fail fast',  but it doesn't seem to be catastrophic.  There are a lot of things going right,  I just need to run the problems to ground.  

I think I will have some time this weekend to nail down the firmware flashing process in a more controlled way, and will get it up on this project page.

Good luck! :)