Mike-- I think you're on the right track here in that you're looking at underwater and overwater profiles rather than CG and CofB. In a well-designed boat subtle trim changes can control weather/lee cocking because they can change the underwater/overwater profiles in a meaningful way. But without casting any aspersions on Patrick's skill as a builder, we don't know how close his hull came to the designed shape. In fact, we do know that the hull intentionally deviated from the design shape.
Question for Mike: Are the centroids necessarily the same as the centers of pressure? I would thing they would be a good starting approximation, although not exactly the same location.
The design change of adding a quarter inch to all dimensions would seem to increase displacement and lower the waterline for a given weight. Unless the boat were ballested back to the design waterline it would seem to make for a boat that might be overly sensitive to trim changes and/or lateral wind forces. I quickly figuring that the extra quarter inch adds between 20 & 30 pounds of bouyency. Might it be a starting point to get the boat back to it's design waterline and then start triming?

Mike Scarborough
Friendship Kayak