What kind of valve covers? If they stamped steel they may have dimples on the sealing surface from over tightening. If they're MP cast aluminum covers then maybe they're hitting the intake runners and not seating properly? I know this is a problem on small blocks where those covers don't sit flat when using aftermarket intakes. They lips that hit the intake runners need to be ground for clearance.

It's got to be the covers not sitting properly. Since it's happening on both sides and in the same locations. Makes sense considering the motor is probably leaning a couple degrees toward the rear as well.