EMC2, Arduino & stepper motors - Have I got this right?
I know I'm a bit late to the forum but interestingly enough I have been working on a open source project called EMC-2-Arduino that can do exactly what you speak of and more...
ie:
  Up to 9-axises of non-blocking synchronous stepper motor control.
  Allow basic E-Stop, Power, Srart, Stop, Pause, Resume and Program Step inputs.
  Software selectable microStepping down to 1/16th step
  Basic serial interface control makes it easy to command via serial a link.

You can find the code at https://github.com/dewy721/EMC-2-Arduino