Have you got a picture of whole back end or as it was before? Is the middle part more pronounced? Does your outboard well have a lip which sits over transom wood/thickness? You need to be mindful of that thickness when making new transom.
You are likely to become very familiar with sanding after this project. It is hard to tell the shape of transom, if you want to make a new skin, you could fabricate a temporary wall of some sort of gloss material like glass or Formica fitted to the back of boat and lay up against it and create the skin that's gone outside in. Gel coat first, then csm, then layup to get thickness again. Likely you would still end up sanding corners and joins though. But def an option if you want to stick with gel coat abs polyester
Alternatively you could get your timbers in place securely Glass from the back, and the front Then shed loads of filling and sanding to smooth on outside. This would be best suited if you are happy to paint the finished surface, and you could build up the inside skin thickness on ply out of boat in your garage..
http://www.westsystem.com/ss/assets/...aintenance.pdf Page 38-41
West specify 12:1 bevel 12x skin thickness at edges where new skin would meet old