Re: bondwood boat help!
Please keep in mind that we are trying to advise you from 'afar' based on pictures only so we can not totally understand your boat and situation. Also, most of us are familiar with rebuilding fiberglass and aluminum boats. In both of these cases even with the wood removed from the boat, it still has its shape.
With the understanding that your boat is wooden and that is only paint on the outside of the transom, it looks like you would need to remove most if not ALL of the rear of the boat. If there were an outside fiberglass 'skin' you would have more of a pattern to work from.
In all repairs you are trying to redo, recreate what the original builder did. In fiberglass boats they layout the outside layers of the hull and then stuff in a wooden transom piece on the inside. To repair that we remove the wood and replace. I think in your case, then entire transom is glued and screwed into sides and bottom of your boat.
You're probably going to need to get more familiar with wooden boat construction. A good website to check out is
http://www.duckworksmagazine.com/index.cfm
As for the splashwell. You can replace it or redesign it as you see fit. I know that without one you're going to get LOTS of water in the boat. My boat doesn't have a splash well and its a short shaft configuration, a 16 inch high transom and I get waves lapping over the back all the time.
Thoughts that I have on your project are:
The main - structural wooden parts of the boat need to be replaced with wood. Marine grade or A/C grade exterior plywood. You can seal and water proof the wood my coating it with epoxy. Do some searches on this forum there are LOTS of threads that discuss this.
The splash well and other not so structural parts can either be wood, metal or fiberglass. When I get around to adding the splash well to my boat, the plan is to use Masonite or hardboard, or even thick cardboard would work, as a form for a fiberglass construction.
I plan to tape, or tack or staple or clamp the form into place and wax it so the resin's won't stick, or you could use wax paper or plastic. Then start a layup of fiberglass on the top of that, layer of mat, layer of cloth, layer of mat, layer of cloth until I get up to about 1/4 inch thick. To finish it off I will probably paint it.
On the on the other hand if I could find the right supply for Aluminum and could put a nice edge on it I could also see using aluminum to build the splash well.
The only consideration is that your outboard must clear the splash well when its up.. The only design data I have found on splash wells is a very old, 1960's document from OMC:
http://www.duckworksmagazine.com/05/columns/max/4/long&short05.htm
Let us know how things are looking..