Motor configuration takes one parameter PER AXIS... (Each extruder can be considered it's own axis)
So for the Z configuration, M584 is the only line that should have a colon (:) seperated parameter for Z.
So for example, this fixed my issues
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; Drives
M569 P0.0 S1 ; physical drive 0.0 goes forwards
M569 P0.1 S1 ; physical drive 0.1 goes forwards
M569 P0.2 S1 ; physical drive 0.2 goes forwards
M569 P0.3 S1 ; physical drive 0.3 goes forwards
M569 P0.4 S1 ; physical drive 0.4 goes forwards
M569 P0.5 S1 ; physical drive 0.5 goes forwards
M584 X0.0 Y0.1 Z0.3:0.4:0.5 E0.2 ; set drive mapping
M350 X16 Y16 Z16 E16 I1 ; configure microstepping with interpolation
M92 X160.00 Y160.00 Z1600.00 E400.00 ; set steps per mm
M566 X900.00 Y900.00 Z30.00 E120.00 ; set maximum instantaneous speed changes (mm/min)
M203 X18000.00 Y18000.00 Z1200.00 E1200.00 ; set maximum speeds (mm/min)
M201 X1600.00 Y1600.00 Z800.00 E250.00 ; set accelerations (mm/s^2)
M906 X1400 Y1400 Z1400 E800 I30 ; set motor currents (mA) and motor idle factor in per cent
M84 S30 ; Set idle timeout