Microstep issue?

1000 RPM is rather fast. As I stated earlier, the faster you go, the less torque you produce. It would appear that this is some sort of mobile application so you are trying to work with the power you have. For full steps you might look into a simple transistor based driver with less intelligence, though you might have to make provision for current limit when not moving to avid heating your motors. For that you might need a motor with a lower voltage rating, but 12V or lower rated steppers is not anything rare.