Transom before core

See how the core was put down first and stringers, transom, etc afterwards

 

Keep cutting back the core and stringers until you find clean and dry balsa.
I’d skip recording the bottom, just taper the edge and glass over it clear to and lapping up the transom.

 

Thanks for the attention everyone, I removed everything from the boat, cut the floor out, cut back the stringers, I think I have a plan for what I am going to do now. I was over thinking it, feeling initially it would be a smaller repair area, but once I cut open the floor and removed everything, even with a now bigger repair area, it will be easier for me now with everything exposed.