Power to open source hardware! Thanks for sharing!
So you are using ATMEGA32U4-AU? Isn't sparkfun micro pro using the MU? I'm interested in working with this processor (AU so I can hand solder). Where did you get the EAGLE part? Just asking.
Oh, I guess you have 3 (or multiples of 3) purple boards for each revision? 
What about the micro SD slot? Would you be willing to provide some information?
I am using this one I got from dipmicro on one of my designs. The pins are not very long so I struggled a bit with it while learning (burning stuff of course) SMD soldering:
They are restocking in a week or so.