Hey bro... couple of things.
Based on what you're saying, you probably use this boat a whole lot, but maybe not for racing? Well anyway, having jacked hull bottoms isn't good for speed. Some pics of your hulls might be helpful but try this...
In your case, what I might go ahead and do is take an angle grinder and clean out the areas where the glass is "folding in."
Get yourself probably a gallon of West System epoxy resin and some fast & slow hardeners, as well as some high density filler.
I'd lay a couple layers of glass (maybe 3-4?) flat across the hull (don't worry about the template, just make it as easy on yourself as you can.)
Then use the high density filler to fair the hulls to whatever template you want, if you want. Otherwise just smear it over the glass to fill in the weave (and be sure to make it thick enough that it'll protect the weave for a while.)
I've done some glass work with my buddy and posted sort of a journal on my website.
www.JaimeZX.com Don't worry, it's not as bad as it sounds.