@morf33 your config looks ok, but for Y you must verify M92 X100.00 Y100.00 Z400.00 E409.00
Maybe the steps/mm is different, verify the count of your teeth, it may be different.
16 teeth: 200 steps per rotation * 16 microteps / 32 mm per rotation = 100.
20 teeth: 200 steps per rotation * 16 microteps / 40 mm per rotation = would be 80.
Seems you have 20 teeth at the Y stepper and with the M92 you get more distance than planned. (16=>20 is 1/4 more, 20/4 mm is 5 mm more, this would match).
I would also change M557. You should take into account the probe offset and start M557 with x40 and Y50. I would use more points for mesh compensation (S value lower or use the P parameter), but it depends on how flat your bed is, i.e. how important mesh compensation is for you.