I have used the Shapeoko 2 for MANY PCBs and I was just covering that subject the other day on my visit to the Inventables office with their R&D guys. I use a program called Flatcam http://flatcam.org/
It does a great job of setting up for files for milling on the X Carve or the Shapeoko. It will produce the needed Gcode.
It is rather easy to get very good boards off the mill with rather little effort. Here are a few samples.
Flatcam will take your gerber file and let you make the needed Gcode toolpaths for each layer on a single or double sided board. Then it will let you set the board cutout and also copper clearance if desired. Best of all it is FREE. If you team it up with something like a TinyG and Chilipeppr or a MK3/4 from PlanetCNC you can even map the FR4 board and account for wrapping of the board and have perfect traces every time.