Man o man, this is making me relive my 3 yr Tsunami restoration.Great to see that you are documenting the project with lots of photos.
They are just awesome boats, and although the work to restore is brutal,but the end result far outweighs the back breaking process.
The old saying "quality is remembered long after cost is forgotten" holds very true to these great hulls.
I think doing the transom from the inside as you are , is the best way as you dont compromise the integrity of the hull.I also did my transom from the inside, I made the cuts in the middle of the hawse pipe cutouts, pulled the rub rail back to amidships, and lifted the rear cap off.
Kinda wished I went with the coosa like you did instead of marine plywood.these boats are stern heavy so any weight savings in the rear, is a good thing, especiall with the weight of the I/O and engine.
Since you are doing the work with epoxy, you may be better off making your own putty for the radius at the inner transom face to hull joint.you could mix up some epoxy resin with some cabosil and some milled glass fibre.it would make a nice strong putty that you could easily apply with a nice radiused edge.
I did the glass layup with vinylester on the transom to the hull, and used hull and deck putty from Merton Fiberglass
www.mertons.com although it wouldnt work in your case , as you are using epoxy and the hull and deck putty is a polyester based putty that wouldnt cure properly over an epoxy resin
Looking forward to your progress, keep the pics coming, and thanks for sharing and saving another awesome classic.