It's plausible.  Because of the jigsaw-puzzle assembly of the Wood Duck 14, it's not as easy to change cockpit sizes as it is on, say, a Chesapeake-series kayak.  You'd need a new "cockpit apron" with your smaller cockpit opening in it.  The apron itself would remain the same size to fit the other deck parts.  

   I'm building from plans not a kit....so it should be almost a non issue right?

Planning on cutting the deck pieces this Sat...wish me luck.....