Without trying to decide if .28+" bed of epoxy putty is too thick to set the intake in, or trying to build the hull up thicker with fiberglass mat, you might consider using some aluminum bar as a spacer. Cut and drill the bar to match the intake mounting flange. Trial fit (of course) using the corner leveling bolts in the intake. Then apply a good coat of epoxy putty to the intake flange, the aluminum bars, and the hull (to make sure there are no voids) and set the intake.
Brian