Hi, the 'clunk' sound is most likely the motors shutting down. This could be caused by overheating of the driver (overcurrent). I would disconnect the motors from the axis and run a job to see if it works ok without friction. You can also slide the axis manually (only do this with the motors disconnected mechanically or electrically) to see if they are smooth and free.
The other problems could be related too, so I would start with the above.
Zax.