I'd be more worried about the uncured gelcoat you haven't found. What are the odds that it is only in that exact spot? If not cured by now it will never cure and rear its head later. I would go for a new body. If replacing the body is not an option, I'd fill low areas with 3M HSRF and finish with normal body filler products. If super deep, I'd fill with 1/2" chopped fibers and vinylester resin, then bodywork as normal.