Certainly a non-microstepped motor seems to run really roughly. I haven't studied it that closely, though - that was on a different machine which had been set up without microsteps for initial testing. The other thing to take into account is the pulse rate you can get out of the driving PC, though. Too many microsteps and you can't drive the pulses fast enough for decent speed. However, most people seem to be using external motion controllers these days which takes that whole issue away.

I did play with the autotune, although I was never quite clear about whether it should be done on load, and if so how you handled the case of a master/slave axis setup. Not a lot seemed to happen, though, and I have no idea whether or not it made a difference! I just use the machine, and it seems to work fine as it is. Might not be optimum, but I'm not sure what difference tuning makes. No apparent resonance over the speed range I use (typically cutting at around 3000-3500mm/min in wood or polythene) and 5000mm/min rapid. I guess that the ideal tune might allow slightly higher accelerations, but like a lot of people I just tweaked and tested until I had reasonable and reliable results.

Good luck - you seem to be getting close now!