[tsubaki]

Welcome to the site.
To me it sounds like a redo (once again) of the transom is needed, to be done correctly and finished correctly, especially of you need a taller transom.
There are a lot of threads on this site that covers transom rebuilds, different approaches and materials. Personally I've always questioned if it rotted once why are you going back with wood again?
My first floor rebuild was useing pressure treated plywood and that was a huge mistake. The glass wouldn't stick to it and it was always "spongey" feeling, yet it didn't rot.
Search the threads in "repairs" and "modifications".