Zach,

First fiddle with the bulkheads a bit.  How does the top of each bulkhead match up with the sheet line.  You may want to elevate the bulkheads slightly to get a better fit there and to split the difference between deck and bottom.  Do they need to move forward or aft just a little bit?  Filling a 1/4" gap w/ thickened epoxy would not bother me, 1/2" however is a bit much.  Hopefully you will hear from others who have faced this problem.  My Shearwater is ahybrid so my actual deck fitting was a bit different.

Paul

I had a fairly large gap on the top of the rear bulkhead on my Shearwater 14 also (I moved the front bulkhead and made a new one so it was a custom fit).  I put a piece 4" fiberglass tape, soaked in epoxy, along the top of the bulkhead that spanned the gap.  When that hardened I filled the gap from the opposite side with thickened epoxy and smoothed it.  Seemed to work fine, and gave the thickened epoxy something to hold on to.

Kathy

Paul and Kathy - Thanks for the help.  I pulled the stitches tonight and I think the filets and tape (per Kathy) will fill the voids.

Paul - in thinking about your comments, it seems like the bulkehead may have been designed with the hybrid deck in mind.  At least on the S&G version, there's really no way to move the bulhead forward or aft because it largely forms the top panel.  Plus, my bulkhead's top is already in contact with the top panel of the deck - the side panels where they meet the top panel is the issue.  On the hybrid, I suspect that this isn't an issue since you can make a more rounded deck. 

 Anyhow, I think it will all work out just fine.  It's interesting that my hand drawn/cut day-hatch bulkhead will be (by far) the best fitting of the three.  It gives me hope to learn that a CNC machine can't always beat a few basic saws, a block plane and a bit of "eyeballing"...

I'm haning a great time seeing it all come together.

-Zach