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I found that the retraction speed was too fast for my z-axis. (old shapeko). The problem is that the original code used the 'rapid' setting for retraction. The default rate of 100 was too fast for my poor CNC. It missed steps and didn't get to the clearance height and screwed up the job (chewing up lots of wood along the way)
I initially thought that I could use the plunge rate for retraction, and that would work. But it seems like we need another knob here that is analogous to the 'rapid' setting, but just for the Z axis. This would be used when ever we move in the Z direction while not cutting. The two scenarios are retractions, and initial movement to the origin.
The initial rapid-Z is set to double of the default plunge rate. (Maybe there's a better option?)