Ryan,
I just finished doing that to the couplers. I was surprised that the coupler was quite a bit down the stepper shaft, and the drive screw was inserted just about 3/8 of an inch.
The first Z homing went fine, and there is no chance of the brass nut hitting the coupler.
Matt,
I have it set at 1mm (down from 3mm) but the surface is very flat, and I don’t think that is the problem, BUT I’ll raise it back to 2mm, for the next cut.
Mike
Edited: the screws are lubed.