Thank you Jeff,
It sounds like you have been going over every bump in the road that I did. 
Only difference is I started with the controller and worked my way outwards to the mechanical bits. I also knew from past projects that once I learn to make something ( like EMC2Arduino ) I end up learning some new things along the way.
I wrote EMC2Arduino as a pilot project to learn how to make a working DIY CNC.
These days as I get time, I'm working on writing HAL2Arduino to make it even better, to refine what I have learned and distill those ideas into less complicated easier to use / easier to understand project.
When I'm done I intend to make a customized live linuxCNC CD that will have all the tricky bits in place so people won't have to worry about it. That way all they'll have to do it play with is the Arduino.