Well, i have finally got my stepper extruder working! With some help from IRC and friends, i have finally made the pololu PCB – a one sided design which has a single wire on the top board.
connecting it to gen 3 makerbot mobo it works straight off the hat with x y and z axis, so for this i am really please, however for the extruder it took a bit of bodging with firmware and machines to get it to work. Turned out that the thing was a problem with repg 25, but i seem to have it working now after adjusting the various settings and maybe a loose connection or 2.
so anyways, the PCB is: