I'm a novice.  My only build has been a wood duckling, which is a close cousin to the shearwaters in design.  Looking at the parts list drawings, it seems like the aft deck piece of the shearwaters is meant to be rounded in front of the cockpit (rather than pointy) where it meets the forward deck piece.  Is it possible that the CNC cutter left a nub behind that you haven't yet fully removed at that spot?

The only other thing that comes to mind is that the forward deck piece curved down a lot more than I expected.  I felt confident that the deck joint was roughly right only after setting the deck on top of the hull and getting them to match up pretty well (which inspired some wire adjustments if I remember correctly).  I'm guessing that you've already done that, but just wanted to suggest doing so if not.

It seems likely that you'd be better off sanding off the point on the aft piece to get a nice smooth interface since thickened epoxy can right any small wrongs (gaps) there.  The main thing is getting the forward deck bent into the right shape.

   Thanks for the response.  I disassembled the deck and did a little sanding.  There are still small gaps but the overall fit is better.

Onward!

It's buried somewhere on the Tips for Boatbuilders section here that, with stitch'n'glue technique, small gaps aren't a Big Deal. The CNC technique for fabricating boat kit parts isn't traditional and alongside the advent of epoxy adhesives gave birth to a wider field of prospective builders not accustomed to traditional woodworking - let alone boatbuilding - craftsmanship where nothing is ever straight & plumb and glue joints need to be virtually seamless and clamped TIGHT to have any hope of success.

My first foray into boatbuilding 50 years ago was a stripper scow from plans offered by Popular Science magazine. Lumberyard plywood bulkheads & polyester resin over strips edge-glued with resorscinol got me out onto the water with friends for a few years. Didn't last though due to the materials used and being stored outdoors year-round in the midwest.

While assembling my second adventure, a CLC Waterlust kit, I had frequent conversations with the designer on many topics, one of which was precision. He allowed that with Stitch'n'glue "... an eighth inch is close enough!" so there's that.

Where possible I strive for a traditional seamless mechanical fit whilst keeping in mind that, with epoxy, one must be mindful to loosen clamping so as to avoid starved joints. Sometimes a sixteenth has been close enough, as I'd planned on 100% painted finish anyway. 

If your aim is a 'bright' finish in the end, and you're confronted with gaps that can't be closed by careful attention to tweaking stitches before epoxifying everything or where possible slight reshaping of the parts involved, oftentimes a "Dutchman" (filler piece, carefully fitted) is a viable solution over simply filling the gap with thickened epoxy.

   Thank you for that input.  For a novice it can be difficult to know whether to obsess over an issue or accept it as "within limits."  If an eighth inch is close enough, I'm good to go.