Can you pull the wires out? If so put a small amount of medium SG on the wire and push it into the hole. Another way to tackle this would be to make boots that fit in the hole and are even with the valve cover level and then cement from underneath like Mark mentioned.
Actually I was half right. That piece and the trim all along the side to the back and half-way in to the door is on the newer tool 55 chevy that Monogram tooled in the '90's? Pink and gray on the box and there was a pace car version. HTH
Carefully mask off the area and apply a small amount of putty or even some of the brush-on putties Tamiya makes. Build it up and sand carefully. Accidents like this are common when scribeing to deepen or create panel lines.