The click you hear and can feel is due to backlash in the motor gearbox. This the Oriental Tapered Hobb motor which ShopBot and others say can be adjusted, I have tried and can't seem to find the sweet spot between zero lash and loading up the gears. This is from Oriental's website, this should give you an idea of what is going on.
http://www.orientalmotor.com/stepper...gearheads.html as far as the scarring on the pinion shaft, I would just clean it up a little with a fine file (I didn't say to make a flat spot) just remove metal that may be raised on the shaft. If the key is damaged, do the same or get a new key. I hope this is of some help...joe