A stalled stepper motor will make a sound like an over running clutch, sort of strange I know but that's what they do. I don't think you have a motor problem. It might also be jerky on a bench without a load on it, expecially if it is using higher voltages. Put it back in your machine and fix the limit switch and see if it works ok now. BTW, never pull a stepper motor apart, it somehow messes them up, and all documentaition I have seen says this as well. Good luck.
DaveA.