Hi Jason,

Bode plots are maybe ok, not sure. Average 75hz and 35 deg results, but that is unknown if accurately applied. I can achieve over 45 degrees with some input values and down to mid 20's with others. I definitely need some guidance on the bode plotting to use it effectively. After re-reading the dynomotion documents, I am still left with ambiguously useful values for amplitude and frequency. Being able to run with stable results from "any frequency" is a bit infinite for me. Other than using as large of an amplitude as I can to achieve measurable results, I am not sure what is applicable. As far as frequency, what range is determined relevant?
75hz and 35 deg sounds good. But unfortunately Bode plots only tell the truth if the system is linear. Linear means that if you inject signal A into the system and get some output and inject signal B into the system and get some output, then if A and B are injected at the same time then the output will be the sum of the independent outputs. Or if A is injected and Y is the output then if 2A is injected you will get 2Y. Unfortunately for most systems this is only roughly true for certain signals. A common non-linear effect is friction, A might cause no response and 2A might cause a response. If the system were linear the Bode plot would be the same regardless of the type or level of stimulus. So the Bode plot should only be used to get some insights into the system and not an absolute guarantee of stability. If there is any frequency and amplitude where the system has a gain of -1 it will likely find that frequency and amplitude and oscillate at that frequency and amplitude.

I ran a few parts and the machine did some better than before, but not good enough. About half the cut looked very awesome, then chattered in the rest but not as bad as before. The good news is the oscillation has become more predictable and other performances of the machine have improved. Now, when jogging with an analog joystick, I can see a resonating shutter at some speeds fairly constant. That appears mostly on my X, with a little on the Y. It also appears different in the + vs - directions. While this does more clearly appear a tune issue, it seems to be triggered by machine stiction and other resonance. My plan is to use the step response move test with various velocities and a travel that will go longer than 3.5 seconds, but will allow more capture of the trouble frequencies/speeds. From there I hope to be able to try other tune and filters to find a more effective solution. That seems like it might take some time with a modest chance of finding a one size fits all solutions.
You might use the CaptureXYZMotionToFile.c to see exactly what is going on while cutting. You might modify it to trigger on larger following errors. You also might set the following error to a very small value to see if the system ever faults.

Testing various speeds and positions also sounds like a good idea.

Maybe tuning for high stability rather than accuracy might be something to try,