The fourth version of the board is finally in the mail from assembly. 

The major change is that the DC-DC Switch Regulator Controller has been changed to a more modern and smaller version than before. I had issues that when the old one (TPS54331) went into low power "eco-mode" the output ripple sky rocketed to 100mV. The new controller (TPS54308) has no such features and should be more stable. I'll try the TPS54302 as well, same footprint, has the eco features and is a lot cheaper.

I have made some changes to the thermistor input subsystem as well. The construction for filtering was totally broken and had massive noise. 

Despite all these power/analogue issues all versions of the boards have worked perfectly fine. The klipper firmware has been tested and runs well on all kind of questionable 3D printer boards, far worse than this board.