Wood boat? Remove the shaft epoxy
a wood dowel rod about 1.5 mm (.0625 inch) smaller than the diameter of the shaft log and about 150 mm ( 6 inch s) long. remove the strut by drilling out the bolts. plug
the bolt holes with dowels and epoxy
then screw and epoxy wood plank, the same dimensions as the foot of the strut, into the recess where the strut was. preferably using the same wood as the hull has. if not a comparable hard wood. also the thinner the glue in the mating surface the stronger it will be. and make sure all surfaces are dry.
Why cut out the cockpit sole? On the inside where the shaft log comes out? that big hunk of wood? that is more than likely the Keelson...ie...the back bone of the boat. Be happy you have all that room that the engine
took up and still have a sound vessel. Not to mention if you follow the above, it'll be les work and cost. I'd only go through the sole if it had rot