If you buy a kit, there is really no way to change the dimensions of the boat.  All the plywood is precut and the 3D puzzle will only go together one way. 

If you buy the plans, it is at least theoretically possible.  You would have to modify the drawings for the sides, deck, bulkheads and/or forms.  No doubt that you have the skills for the woodworking part of this, but creating a new 3D puzzle that fits together is a harder problem, and also making it look ok is even harder.

If you are absolutely set on the SW16, you could go with the hybrid version.  It would be relatively easy to add height to the forward forms to make sort of a "high deck" version.  I am not sure how it would look.

Honestly, your best approach would be a different design with more foot room.  I see a number of good boats that will fit your feet - SW17, SW Sport, Petrel Play - L, Night Heron High Deck......

Ditto what Mark N said.....   

the stitch and glue shearwaters all are 'exact-fit' kits.   their construction approach does not allow for any real modification of hull or deck shape.

as mark mentioned, it is relatively easy to modify the deck height of the hybrid version becuase you will be constructing that deck....it is not pre-cut.

and, of course, there is just go with a design/kit that would accomodate your feet....and mark gave some great examples.

i've built a shearwater 17....and they are very pretty and versatile... and that is how i would solve this problem with the least hassle if you were hooked on that design.   below is a picture:

i have also modified decks on several boats with strip build decks.....it can be fun to do....but does take some planning and set up to get a good result.  the picture below is a night heron that has the foot room of the high deck version but the deck is customized to have a petrel-like look.

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   alright, thanks for the advice I will look at those other designs. This forum is a great resource! thanks again