Motor tuning and switches

[JAZZCNC]

Just so I know, how would you describe the observable characteristics of a motor which is running "rough" as opposed to one that is running well?

Now that is a difficult one to answer because it's more sound than visual, thou it can be seen at very low speeds. Rough would be growly low pitch sound and notchy action to movement.
Nice running motors will have higher pitch hum and smooth action. Running a motor at really low speed ie 50mm/min for test is a good indicator. Nicely setup motor will smoothly turn, rough running will have a notchy action.

The machine and how it's built can play big part in how motors react with different micro stepping . Resonance of the machine affects how motors work and different frequency's don't always suit some Micro stepping settings so it's not uncommon for higher settings to work worse than lower settings or vise versa.

It's all about finding a balance that works best for your machine. To be honest with newer Digital drives Resonance is becoming less of a issue has they are so much better at handling resonance. But not so long ago with old analog drive technology resonance could reduce a motor to perform at half it's capabiltys and for people to not even know they had a resonance issue at all.!! . . . To a trained ear it was obvious but not so if your not aware of resonance.

If you want to experiment and get a feel for how Micro stepping and Resonance affects your machine then play with different MS settings and tuning. This way you'll find the sweet spot that suits your motors.
Resoance is also one reason why you can't run or tune a motor on the bench. It's very common for motor just sat on a bench to sound like a bag of marbels and jump all over the place but run sweet when bolted down.!

In the Motor Tuning window of Mach3, should the "step pulse 1 - 5 us" and the "dir pulse 0 -5" be left at zero? How do those values affect performance.

This depends on the drives you use. Some drives will state direction pulse be so many micro seconds in front of the Steps or vise versa but in general just leave at 0. If you feel your lossing steps then playing with these settings can help.