Are you familiar with these?
$3 – Direction port invert, mask
This setting inverts the direction signal for each axis. By default, Grbl assumes that the axes move in a positive direction when the direction pin signal is low, and a negative direction when the pin is high. Often, axes don’t move this way with some machines. This setting will invert the direction pin signal for those axes that move the opposite way.
This invert mask setting works exactly like the step port invert mask and stores which axes to invert as bit flags. To configure this setting, you simply need to send the value for the axes you want to invert. Use the table above. For example, if want to invert the Y axis direction only, you’d send $3=2 to Grbl and the setting should now read $3=2 (dir port invert mask:00000010)