Well my glass guy has been feeling bad since it's been so hot so I went over to help get it going. Got the skin off and wow the smell. It was bad. Had some dry wood in high places but probably 85% was wet. It would seem someone put a full new transom with the 20" dropped area at some time. Then later someone put a section to build it up to hold the 25" motor.

You can see the rectangle section at the top where they updated the transom to 25". The inner piece of wood was cut exactly to the shape of the dropped section. The the outer piece was cut a bit bigger to overlap the seam.
I suspect it's not the original transom as it was cut about 2" smaller than it needed to be. Then they had some sort of hard rubbery material filling the void from the edge of the wood and the side of the hull. None of the wood had been laminated together and the 2 sheets were put together with crown staples. I'm highly doubt that Wellcraft did that.
Now to the real disturbing findings. On the outside of the stringers where they connect to the transom there were holes cut through the inner skin. So any moisture that came to the stern on the outside of the stringers went right in the transom wood.
Here you can kind of see the hole. This is the starboard side. What really sucks is this also let the moisture to seep into the stringer. But he doesn't think it made its way far into the stringer. Tomorrow he's going to cut a section out of the inner skin and investigate more. And he said it will also give him better access to tie the stringers into the new transom well.
Here's about 1/2 of the nastiness pulled out.
We got all the big stuff out. Tomorrow he's gonna let the rest of the wood residue dry out and hit it with the sander to clean up the skin. Then start putting it all back together. He's going to lay another layer of glass to the inner skin making sure it's sealed up from everything else. He also plans on making some passages from outside of the stringers into the bilge for any water to drain into the bilge instead of the transom.