First, this is not the first time this has happened. I'd bet the folks who teach the kayak building classes at WoodenBoat School see this happen every year.

Second, I'd run it through a table saw to take most of the wood off, then finish it carefully with a plane and plan on painting the hull when the boat is finished.

Or even better, if you're confident of your table sawing abilities, cut the bad sheer clamp off, cutting one or two/100s of an inch into your plywood side panel. You're going to glass over this side anyway, half the area will be covered by a rub rail, and if you don't cut through the outer ply no one will ever notice.