Bummer. Yep, you have to install them with the screws pointing forwards. The fins won't fit in that way.
I suggest razor blading the fiberglass around the boxes and sticking a fin in them. Then rock the fin back and forth to break the box free. You will pull foam out with it so you can either fill the routed holes with Q-cell and resin mix and re-route or stick some fiberglass scraps in the pocket when installing the boxes the correct way to take up the space.
You'll have to sand the foam off the boxes or get new boxes.
Then cap with a layer of 4 oz cloth before hotcoating.