It all ends well. After changing the wiring back to the original (and reversing that of the extruder), and running through the calibration procedure once again, the printer seems to be calibrated. The only cause I can think of is a bad connection on one of the stepper wires before (although they ran smoothly). If one stepper was missing some steps (one of its coils being open circuit) the calibration would not work.
Manually moving to random X and Y locations work as expected. I was also able to run through the bed-levelling calibration procedure. I then sliced the calibration "phantom" supplied with the Morgan data pack, and decided to print it.
The printer works wonderfully, except for the extruder. It is a hit-and-miss affair, sometimes just slipping, sometimes (and with a bit of manual feeding) it drives the filament. But it is not yet right (at least I can work on another drive gear).
So close, and yet so far...
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