Gonna throw this at you, I will probably be proven wrong, but try to leave a small amount of the origional glass at the bottom of the stringer vertically (like an inch or so) but feather it out smoothly, it will give you a lot of added strength when the new beams are installed, otherwise you are relying on the bond of the new glass to old, also may look into epoxy resins, West Systems is really cool stuff and does not have some of the issues of the polyester resins, just a recomendation though, I love the stuff.
Good luck, cool little project and welcome aboard...
GT