Hi,
Has any thought been put to using a Raspberry Pi for the controlling hardware, with a dual stepper driver running from its GPIO pins? Could bypass the need for any arduino at all if all its there for is to drive the steppers.
With a custom PCB, you can include the 5v/12v regulation and power through the GPIO pins.
Not sure on the processing power needed, but the new A+ layout/design is only £20.
Darren.