I wouldn't give up too soon. It looks bad but that's only a rotten piece of ply. Dig it out and score the whole surface of the transom and onto the hull by about 300mm(ish) using an angle grinder. Make sure you get right through any gel coat or other finish on the old glass, if possible you need to get your new resin to bind into the old glass mat. Haul off the tubes and clean up the same way. I know you said you've been asked to leave the tube flange attached but if your tuber is ok starting from scratch shouldn't be a problem. You'll get that done in a morning's work if you're up sharp.
Make a cardboard template of the tansom and cut two pieces of 19mm ply about 12-15mm smaller on the top and sides. Score the ply very raggedly to form a key - raking it up with the teeth of a panel saw works well. You're going to layup onto the transom about 3 layers of 1.5oz csm and fit one piece of ply by clamping it to the wet lay up. A couple of battens of wood and some G-cramps will likely be all you'll need for that. Wait until the resin goes off then follow that with more layup and the second piece of ply - you can either clamp it as with the first piece or screw it to the first piece, (Though putting screws through wet resin and csm isn't as easy as you may think.) you can even just nail it through and remove the nails after the resin is hardened. If you want knees to support the transom, fit them now then layup over the top of all the wood and around the edges and onto the original fiberglass. Layup a good distance onto the deck because that's where the stress will be applied buy the engine.
Get well prepared and you'd see it done in a weekend.
Edit: I've just come across your teardown thread and I see you've already stripped the transom but there's other hull damage too...hmm... if you find another hull cheaply it could be the best route. Hmm...
But there will be satisfaction in bringing it back to life if you continue!