Protecting digital electronics from nearby high voltage sparks
It looks like your problem is the wire that runs relay to HVPSU. That wire conducts the interference straight in to the supposedly screened region.

If you must have a galvanic connection through the Faraday screen, then take it in through a feedthrough filter. 

It's not clear from your diagram what the relay is doing to the HVPSU. It has only a single wire drawn. Where does the return current flow, and is it amps, to power the PSU, or mA, to trigger it? If you want the Faraday screen to work, then it should flow back to the screen at the filter, in a small loop that doesn't magnetically couple to the MCU.

You might be better off simply coupling the MCU to the relay with an opto-coupler. That might be sufficient. If it's not, then reinstate the Faraday screen, with the hole in it bridged by the opto.