Posting to hopefully help anyone else who may run into this issue. Recently finished assembly of my Shapeoko 5 pro. Moved on to testing the machine and was getting some very jerky / noisy movement when the machine was moving the y axis. The machine would also intermittently not be able to properly initialize. I was repeatedly getting HM008 GRBL errors.
My first step in the troubleshooting process was ensuring the squareness of my machine. After I had verified that it was dead on square I ensured that all of the inductive limit switches were functioning properly in the debug within Carbide Motion. Eventually I realized that it was always the Y1 limit switch on the right side of the machine that it could not move off of. Having narrowed the issue down to that location on the machine… I decided to switch the y axis stepper motors to determine if it was a stepper issue or a more complex wiring / controller issue. Switching the stepper motors ended up not changing anything. The issue remained on the right side of the machine. I ended up inspecting the wiring harness more closely and was unplugging and re-plugging things in when I noticed something odd. I had unplugged the stepper motor harness connection from the controller and noticed that one of the wire connections had a bit more silver showing than the rest of them. Tried tugging on it and to my surprise that wire was not crimped into the connector at all. Tracing the wire back to its label, it belonged to the bundle of four wires for the Y1 stepper motor. (Was the blue Y1 stepper motor wire) At this point I knew I had found what was most likely causing me the issues I was running into.
I luckily had all the tools necessary to remove the pin from the harness. Unfold the little crimping portions of the pin. Then properly crimp the wire into the pin and re-insert it into the harness connector. And VoilĂ ! The machine was now moving significantly more quietly and homing perfectly every time.
So, if anyone runs into similar issues / symptoms… A very easy and potentially time saving thing to check is; giving all of the wires in the connectors going into the controller a tug to make sure they are properly crimped / seated into the connector.
Definitely not an easy fix and not something I would recommend most people attempt to fix… But could definitely save some troubleshooting headache for anyone else who potentially gets a wiring harness with a connection that is not crimped correctly.