Welcome to the SeeMeCNC Community

I have been playing around. When I set layer height to 0.04 then the z retract is 0.04:
; layer_height = 0.04
; perimeters = 3
; solid_layers = 3
; fill_density = 0.4
; nozzle_diameter = 0.4
; filament_diameter = 3
; extrusion_multiplier = 1
; perimeter_speed = 45
; infill_speed = 60
; travel_speed = 150
; scale = 1
; single wall width = 0.42mm

M104 P200 ; set temperature
G28 ; home all axes
M109 P200 ; wait for temperature to be reached
G90 ; use absolute coordinates
G21 ; set units to millimeters
G0 Z0.040 F9000.000

But that would make the layers way to small, right?

You are specifying a layer height of .04mm, retraction is something different, it is under retract settings. The Gcode you posted above is the starting Z height, because layer 1 would be at .04, layer 2 at .08 etc....

Thanks,
I'm so glad you are here. Only one thing left, learning how to check the temp on the hot end and we can start printing!!!!
Thanks again.