I use a tevo tornado which is similar in many ways to an ender3 and added a direct drive extruder. I ended up needing to change the wiring for the stepper motor because it just sat there jerking around but not moving. I don't recall if I used a meter to measure resistance or if I just swapped wires until I got it working but it prints perfectly today and has for years.

To do it I think I had to use a small screwdriver to push in the little barb that holds the pin in the connector (on some you can lift a little plastic tab on the connector to pull it out) then I could just push it back in place. Make sure you don't disconnect your stepper while powered, it can toast your controller.