Thank you for the advice, I have very little experience so far as I'm just a hobbyist, this is my first board to test the principle and will probably be in the testing stage for quite a while, hence why I'm inviting testers. Interference on encoder channels is certainly an issue I will look out for. The DCSERVO code uses rotary optical quadrature encoders but I believe a linear arrangement could also give good results in the manner of a DRO.
I understand the reluctance concerning microcontrollers particularly when dealing with stepper motors, but I am hopeful that a closed loop servo system will be quite a different story. Since it operates on a PID it should dynamically correct itself rather than suffering lost steps.