CNC Update
The controller board was finished long ago and I am able to send basic commands to actuate the motors and read the optical encoder strips via Serial Emulation over USB. The trouble now has been writing a specialized USB driver for it. After a while it really dawned on me how involved this is and that I should save that for later and just focus on getting a basic CNC up for now and start making cuts 
I will see what it will take to get EMC2 to talk to the board over the CDC USB serial emulation link.
After catching up with work and school, I need to detail the following:
1. How I identified the pinout for the optical encoders
2. How to read the optical encoders.
3. Provide schematics of the control board
4. Document and publish the source for the basic firmware I am using on the controller board.