Now everything seems to be working like it was when using my stock Ender 3 Pro board.
Print quality is more or less the same, maybe a bit worse than before, but I need to experiment a little more with the duet config and in Cura.
But the stepper motor noise is almost gone they are so much quieter now!
I also had to lower the current for the stepper motors. They where running really hot using stock (x, y, z, e) (725, 725, 725, 900). Trying to find the magic numbers here.
I see everything from 400 to 900 on this forum.