Not sure what you mean there, the noise is the stalling. If the machine has been on about an hour it seems more prone to it. If I was to rewire it any ideas where I can get replacement connectors to fit the blue control box?

Is the nut the part in the housing that the leadscrew tuns to move the gentry up and down? I have tried moving the stepper motor by hand to feel for any tight spots and there didn't seem to be anything that bad.

The stalling can happen anywhere on the y axis, doesn't seem to be related to x or z axis position.