Hummmm, To get the transome looking like the original I think you would have to use marine ply again, don't be tempted to use one solid piece of wood as it will expand and contract too much.
If you can't find the right size ply then you will have to stick several sheets together. Once this is done you could try using biscuits, a biscuit joiner and glue. After that you will need to use fibreglass then gel coat the flow coat.
This will only work if all the load is downwards on the new section and not through it like bolting the engine through the new section.
Why is it cut down? Are you sure you haven't got a mid shaft on there?