I just changed out a axis and I went to mdi and sent $3=2 and it still goes backwards. Thoughts?
Usually the Z-axis goes backwards 'cause the spindle carriage plate is installed upside down — the static pulley should be on the left.
Alternately, one can change the Grbl invert bit as you noted — details on that at: https://wiki.shapeoko.com/index.php/Grbl#Grbl0.9 — changing $3=6 to $3=4 ought to have reversed the Z-axis.
The other possibility is wiring — there are a bunch of ways to reverse a stepper driver, and it’s also possible to wire one up so it will only run in one direction — check that. All the connectors ought to be consistent, the wiring extensions if any straight through. See: https://wiki.shapeoko.com/index.php/SO3_Function_Test#Direction_Correction
If none of that pans out then your Z-axis stepper driver chip may have had a failure mode where it only runs in one direction. Let us know at firstname.lastname@example.org and we’ll do our best to help.
I fixed it. I wired the limit switch wrong lol