I thoroughly recommend you have a look at this guy on YouTube. He's a Canadian boat builder/repairer and has got some really useful tips for glassing etc.
https://www.youtube.com/user/boatworkstoday/featuredIf you have the floor out and think the transom is trashed then I would be inclined to see if the stringers are waterlogged. Nearly all fibreglass boats have stringers to stiffen the hull. They are usually 10mm or bigger ply and run along the length of the boat. In addition there is usually box sections which support the floor that should be looked at. The newer more hi tech way is to put a moisture meter on it but the old fashioned way is to take a bore sample by drilling into the wood and checking the sawdust in the drill bit. If its damp it'll stick to the drill bit.
I doubt very much if the stringers towards the bows are rotten but towards the stern they maybe in which case they will need to come and be replaced somehow.
Sounds as if you are really cracking on. If you time to take pictures that'll be great.
