Sounds like a great project.
For circuit milling bits check out www.drewtronics.net I use the 60 deg bits mostly.
When milling your first side of a board it helps to drill 2 holes through your board and into a spoiler board below, then when you flip the board over you can place pins in the holes to align the board for the next side, this works really well, but there are lots of other ways, I am sure others will share their ways with you.
Also google pcb-gcode for eagle if your interested. I know your not using eagle to design your board, so this may not be any help to you, but alot of folks are making their boards with that combination.
hope this helps!