The body fitting manual for dealers, which I can't remember the name of but someone else will, refers to placing packing between the hood frame and the channels to bring them closer to the glass for a better fit. This is probably going to be your best option. Recheck the hood frame fit, get that as close as you can on the B post and header rail adjustment first, then if it still isn't right remove the sections of seal with a poor fit, peel the hood back, pack them, reglue the hood, fit seals- probably not as easy as it sounds and something I need to do too at some point!