Update, has been slow since I lent some tools to my brother to finish some house work.
I have taken one layer of ply off the transom, and hope to remove the second layer down to glass this weekend.
Ive cut back the stringers from the transom about 3" to facilitate transom removal.
Ive also trimmed the lip around the cap, looks better now

And I chipped most of the potting compound off that held the floor to the stringers.
I would like to get the new transom wood on before its gets to cold to work w/ the epoxy.
Then Ill be adding 2" to the top of the stringers to raise the floor.
Also lots of grinding to do. Ill be happy if thats all completed before the "real winter" sets in.