Yes, getting the skeg box width on the angle is a tough geometric problem. I would get a piece of wood the width of your box and cut the end on the angle of the boat and trace that. Theoretically, the greater the angle of the hull, the wider the width of the cut will have to be to keep the skeg box vertical. Or have someone hold the skeg box vertical and take some scraps of thin poster board and extend down the longer side of the skeg box and trace that.

Also don't forget, you are using epoxy putty and glass cloth so you can adjust for any errors.