Re: Transom dimensions
the little dingleberry they supply for an exterior transom brace parted company with my boat years ago (the flap that held it on was made of the same matetrial as the seat hinges) so i replaced it with a hunk of 3/4" marine ply almost the width of the transom. it's not held to boat at all, just floats loose til i tighten motor clamps. with this in place, i haven't had any problem with excessive transom flex despite being overmotored by 2hp and about 5 lb. relative to factory specs.
i think you have the right approach. kind of like a tinnie, these boats are a tabla rasa that you can/should modify to fit your needs, and the hull will likely outlast lots of the ancillaries. when my seats finally wear out (the pin holes will go first, and i think i can extend their life by cutting brass bushings from short sections of 1/8" brass pipe and gluing em in place), i'll make another set.