most strippers/s&g would be fairly modifiable to achieve this. would look for a fairly wide or low side flare flattish bottom type and if the design sheer is low enough - ok or just droop down a lower sheer strip.
as the new deck only needs to be flat or simple curves, any constant radius curve used betw the sheers as a form will give a deck.
use the same cg placement for your body and draw an outline of you seat and leg shape on a pc of paper w/ say 1" all around and cut out that shape from the deck.
add a drop flange around the cutout like any hatch we do and put in a whole bunch of foam insulation to scoop out a shape, spray foam gaps. resist the flange, maybe the foam and lay a cf cockpit out. let set up and drill 1/8" holes every 6 in thru both the cockpit flanges. pop the cockpit, put anchor bolts in the flanges, ss carriage bolts to hold in place. maybe some foam added to bottom of cockpit and sides for rigidity.
then easy to repair etc.
basically just a hatch cutout but the hatch is cf and dips inward
i would think that guillemots would be a good eg as the sheer is lower than many (wood) yaks anyway.

and the fun will be deciding how complex the outline shape is to be.
and for the first one, maybe disregard scuppers, but could have normal bulkheads and fore and aft hatches too.

but really no big deal at all
take a look at the wave witch for a simplistic example:
http://www.pacificfleet.net/performancenotes/wood_kayaks.htm
-mick