I had mixed results with the milled pcbs. I ended up making three. They all programmed but showed up as a usb device only sometimes. The FR1 boards have a limited rework lifetime so as I would debug and rip off components, I ended up just milling the boards again. I was using some Radio Shack solder so I'm going to try again with some better solder to see if I can make the boards more reliable. Since I was the guru for PCB design tools, I ended up making a simple add-on board that turns a standard arduino into a ISP programmer as an example if anybody wants to learn Eagle. Here is the board and schematic. The firmware is available as an example in the latest Arduino IDE.
Here I am debugging one of the boards and finding a short