So I thought that I'd share the status of my current build, and a nice way of correcting the twist that can occur when stitching the hull together. Keep in mind that the twist can be more of a problem on a planing hull like a surf kayak, and while I haven't read of any issues with the Matunuck, I imagine that twist could pose a problem there.
Things got a little interesting with my build because I had decided to cut my panels on the diagonal of the 4'x8' plywood sheets. All panels were roughly 8'4" in length, and I was not about to scarf for that.
While laying the panel templates on the diagonal saved me the trouble of scarfing, it also introduced a diagonal bias twist into each panel... The wood grain was definitely not helping me at all. Now, with the average S&G kayak hull, you are working with 4 panels, and where they meet in the bottom forms a Keel of sorts, which aids in the alignment of the whole deal. With my planing hull, and the bottom panel wanting to curve on the diagonal, I knew things would be interesting come alignment. I also knew that the problem had to be the grain and not mistakes in making my panels because I matched all the panels up when planing them down to size.
So... I'm sure i am not the first person to do this, but I used a self made piece of twisted pair wire to "tune the boat". When the boat is twisted, it is not square, and therefore can be corrected by tightening whichever diagonal is longer. So with the two wires strung along the diagonal, I tightened this up until the hull straightened up, and the diagonals were equal.
Hopefully this may help anybody in the future, especially if you've cut out the panels yourself and are worried you messed up all of that expensive Okoume~
~Here are some pictures~