Will,
I did this on a 20 sceptre and the area above the hatch and splash well is "glued" up to the transom with a polyester putty. It can be murder if all the wood is in good shape. I had to cut the fiberglass skin on the transom from the inside, and pulled the liner out with part of the transom still on it. Get creative.
Use a dremel tool or grinder to cut in the middle of the notch up the sides. It won't really matter since you'll be re-glassing this whole area.
Hope this helps.