Hang on. Is this any different to how I have been running this machine for several years? I have 2 identical stepper motors wired the same way to identical stepper drivers. They have their own step/dir signals but as these are slaved they should be the same. When I first built it I aligned the motors to full step with loose couplings and have not touched it since. Z axis sounds smooth as the day it was built. Only difference with the update is running off the same dir and step outputs.