I've just read the thread through - yeah, try changing the outputs still, but keep in mind the stepper drivers. In a pinch, I'd try disconnecting the step/pulse input to the driver and just flashing 5v across it (make/break with a bit of stripped wire) - all correct polarity of course. Quick way to check that the driver hasn't been borked along the way. Zero-cost, removes a component from the diagnostics.