I need Transom Help Please!

[NIPPAH]

So I've been rebuilding my 1975 MA, today we got to the transom area and we're hoping we would just have to re-glass the cracks etc. no such luck... The wood in the transom is soaked. In the 80's my Pops replaced his transom on 69 seacraft hull from the inside out. So we started that way. We have cut everything out so far and the whole outer shell is still intact. Looking on this site I'm seeing a lot of people have cut it from the outside and left the inside. Are we doing it wrong? Also at this point it's too late, Lol.
Next question is for the core of the transom has anyone used 1.5" NidaCore board? That's hat I was planning on using. Idk any help/input would be awesome and greatly appreciated. Also I have a 25" 1987 Johnson 140 for power... Do I need to raise the transom? Or can I leave it alone? Thank you.