Its a fresh install of marlin v1.0.0 (according in the data dump on connx to the printer software).
The whole assembly was working (with a 644p chip) until the blue smoke monster and my chubby fingers got involved, I bought a new board, and steppers and installed them today.
This means, I hope that the starting point is pretty clean. I've set the board type, and flipped the endstop location on Z, and reversed Z direction. Other than that, its "as is" off the firmware press...
So to address your questions - I've set the current on the stepper driver, I can only assume this means the stepper driver is working. Also, the motor works OK when hooked to another channel, and the stepper driver works OK when placed on another channel. This leaves the board hardware and firmware.
"check pin assignment" - which pins, and what would be the reference?
"PULL-UP/-DOWN settings" - I'm assuming they are the same as Y, so if this assumption is correct, I will go back and check in config.h.
"proper wiring and grounding" - I'll have a good look around, but I'm reluctant to get too involved without knowing what I'm looking for... thats how the blue smoke monster got involved...