I really like your limit switch design. I have this problem with my Align power feed, I don't damage anything, but it rolls the microswitch box over when I manually crank. I understand you keeping this simple. I'm surprised that you don't feel cogging of the stepper motor when manually cranking this, so this is a good thing. I'm guessing your stepper amplifier has some protection diodes to protect the output transistors. I'll have to keep that in mind and check that with my future install.