!need Help CNC6040Z USB Limit switch wiring!

[Doddy]

Assuming you've setup Mach correctly (particular the motor tuning, with sensible accelerations and velocities - keep it simple/low performance - 100/400 respectively to start with, and 5us pulse-width)

Swap the output wiring (plug on the card?) from the X axis with the Y axis, to see if the problem is truly related to one channel on the controller (i.e. if having swapped the wiring the X-axis starts failing then the problem likely lies with the board). At that point you're limited to checking DIP switches etc on that channel - or full blown fault finding which I guess is likely outside your comfort zone given the nature of this question.

If you had access to a scope, I'd be looking to trigger/display a waveform on the step pin on the input from the 25W D-type whilst monitoring the CLK (pin 3 on the TB6560) to check that the signal was getting through cleanly. Then verify the signal on CW/CCW pin (pin 21) to verify that's clean - though that is not indicating a problem from your description. If those signals are clean, then the problem is either with the TB6560 or the PCB itself - visual on solder pad/dry joints.

If the signal on the step-pin is good (it should be - if not look back up your chain from the parallel port cable to PC) and the CLK pin on the 6560 is crap, then you need to look at the performance of the opto-isolator that decouples the parallel port to the controller.

Edit: Added a missing bit:

If, having swapped the axis, the Y axis still fails, then look at the integrity of the wiring from the board plug to the motor. Check for continuity between pin-pairs, and no continuity between the pairs (i.e. pins A+B = low impedance; C+D = low impedance, A+C = high impedance... just up to you to find the mapping of A,B,C,D onto the plug). If that's wrong - then it's either the wiring at fault, or the stepper itself.