After consulting TAF the solution for the misalignment was up-sizing to 4.8 mm rivets.
I’m referring to this this misalignment: Match-drill RF skins
TAF confirmed that the tail-hook wasn’t exactly correct and therefore was pushing the left side of rib 8 more backwards.
A piece of wood was used to put rib 8 straight by pushing the right side a bit backwards as well:
On the skins the hole is elongated but acceptable according TAF:
By adding and removing the skins, and up-sizing the holes some scratches occurred at the skins, so I re-primed this parts: