Sorry for saying that but generally polyester guys have not the knowledge background about the chemical interactions between wood/plywood and polyester resin. A 60 years experience tells these two materials are promised to divorce and after some time there is a very poor adhesion between the GRP skin and the wood.
For prolonging the boat life for a short time there is a very amateurish fix, which needs only patience and few tools. Disclaimer no pro would use that as the results are at best mediocre but for a boat used only in calm weather on a nice sea near the shore that can work.
The first thing is to a fix of the transom an essential structural piece and absolutely needed for the waterproofing of the boat. It's rather easy and that will give you a taste of the job to do.
First step is just to cut the external GRP skin of the transom, leaving around 8 cm at the top and the sides so the glass joints with the hull are not touched. Use an 4" angle grinder with a diamond disk or simply the thin disks for stainless steel. Peel the skin with the help of a wood chisel. You'll be surprised how easily it will peel.
Now you can assess the extension of the rot and the general humidity of the wood. You may be surprised by the degree of humidity of the wood. Take out all the rotten plywood gently with a good margin into the apparently good plywood. Clean up very well.
Make holes diameter 1" 25 mm, depth 2/3 of the plywood thickness. Take care not going too far and piercing the internal GRP skin. Pattern: a grid of holes spaced about 3" 7.5 cm starting close to the GRP strip. These holes have two functions: to help to dry, to create a mechanical key between the outside skin and the plywood.
Let it dry slowly, protected from sun, you do not want any warping or checking, as only one face is exposed to dry. That can take some time at least one week, maybe more. Resist to the disastrous hot gun itching, be patient. An ordinary fan helps a lot.
When dry, repair the missing rotten plywood with pieces of external or marine plywood. Do not use any epoxy glue which inhibits polyester, use simply polyester resin with a bit of cabosil. There is no need of a very strong glue. Glue well specially to the hull and the inside skin.
You are going to make a new external skin. You have several possibilities but I'll describe the simplest one.
With the angle grinder and a sanding flap disk grit 60 or 80 sand and bevel the 8 cm strip of GRP that remained attached to the hull. That will permit to make the joint between the new skin and the hull.
Impregnate all the holes with resin diluted with 10 to 20% styrene with a good dose of peroxide, about 1%. No other solvent only styrene which cures with the resin. Impregnate until the wood refuses to suck the diluted resin. Immediately fill the holes with a sauerkraut of chopped glass and bit of aerosil to control the thixotropy. Fill well with no air bubbles and let it protrude of the surface of the plywood. It's ugly. It's a messy job, do not worry.
Let it cure well, at least 1 day.
Now sand the plywood and glass plugs with a 40 to 60 grit sanding paper. The surface must be rough to give a mechanical key on the plywood, but perfectly flat.
Now glass the transom. It's a classic lay up of mat and cloth until you get the good thickness.
Finish the job and paint.
After you can see how to fix inside, you have learnt the basics.
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