Cutting a piece out of the middle of the hull should be no great
challenge. Just be careful to choose the locations of the joined halves
that they match exaclty. Then sand off the inner surface around the cut
and apply a couple of layers of fibreglass soaked in resin through the
cockpit. Boat builders call it a "butt" join. I've used it in plywood
boats. While the boat is in pieces it should be easy to prepare the
inside, move the foot braces, etc.

The challenge would come in enlarging the cockpit. I don't see how you
can cut a piece out of the middle of a kayak without effecting the
cockpit, and they tend to have moulded coamings to keep out the water
and to allow a spray skirt to be tied on. Before cutting I'd want to
figure out what to do about the cockpit.