I had the same problem with my Petrel.  I used Carbon fiber on the interior in the cockpit area.  Several days after  glassing and filling the interior, the hull came in almost 2 inches in the cockpit area.  I emailed Joey Schott at CLC, and he said try putting it in the sun, then put in spreader sticks to get it back in shape.  I followed his advice, and I was able to get it back to the proper width.  The deck did just the opposite, and expanded in width.  When it came time to mate the deck and hull, I put both outside, in the sun, with the spreader sticks still in place,  and warmed up both  pieces.  They went together much easier than I expected.  I did use a flexible putty knife to either pry the hull out were needed, or squeeze the deck in.  I also adjusted the spreader sticks as needed to help align the two pieces. If I remember correctly, I put the deck in place as far as fore and aft, then started from the center, working side to side.  The center is more flexible than the ends.  It was the only part of construction where I had another set of hands, which also made it much easier. When you think about it, the wood is still fighting to go back to straight, after we have bent and twisted it into a desired shape, with other forces pushing it in other directions.  I used the filament shipping tape to hold them together, as shown in the videos, and decided more was better. I think I used 4 or 5 of the smaller rolls. I would put one strip on, and there would be a small adjustment needed, I would tape right next to the first piece, and take up the slack from the adjustment.  Duct tape will stretch, the filament packing tape doesn't. I envisioned an explosion of wood strips, but with the glass tape over the joinst, it looks just like it should, and appears to be very strong. 

I had the same problem and it's happened to others on this forum. The problem is that when fiberglass cures, it's shrinks and that can cause stress on the underlying wood that can cause it to bend in the direction of the new fiberglass. The hull, especially in the ends where there's a deep V shape, wants to close like a leaf and become more narrow, while the deck, which is by comparison relatively flat on the ends, doesn't draw together very much.  

Try measuring out the width of the deck and cut some spacers and fit them inside the hull to stretch it back as much as possible. I found that it will relax in most places, and hopefull it will return to its original shape. It worked pretty well on my Petrel in most areas, but I spent three or four days stretching my hull back into shape.

After stretching, I found my stern was still about a quarter inch too narrow. On my Petrel, the deck of my stern is pretty flat and so the wood there is basically lying flat on the shear strip. That means the wood there is not mated like it is on the rest of the kayak, and if I sanded it to fit, the only problem was that I was cutting through the fiberglass. So I just sanded it to fit the narrower hull. There were a few other areas where there were minor misfits. I just sanded them even and then layed a strip of the fiberglass tape on my edges to cover the newly exposed wood. 

It's not great, but it's the best I could figure out. 

Thanks for the advice!  I like the idea of spreader strips and warming the kayak in the sun.

I did not know that the epoxy would shrink.  I wonder if the problem was caused because I put some thickened resin in the bow and the stern.  It was probably only about an inch thick along the bottom of the "V" of the bow and stern.  One of the final steps is to fill this area with thickened epoxy.  I thought that because I had access now, I could better bond the cedar strips to create a stronger kayak, and make it less likely that directly hitting something would put a hole through the kayak.  I'll have to put the kayak back on the forms to see how its shape has changed after fiberglassing.

I'm also wondering if I can install shear clamps along the inside of the joint.  I've used shear clamps to join the deck to the hull on stitch and glue kayaks.  I'll have to look at the shape of the kayak on either side of the joint tonight to see what I can do with a shear clamp.  Because of the curved shape of this joint, maybe I can use short one or two foot strips that are either touching each other or have fiberglass tape between.  A shear clamp seems like it would create a stronger joint than just fiberglass tape.  Has anyone used a shear clamp to join the deck and hull of a cedar strip kayak? 

Is there a way to prevent the warping of the kayak shape during fiberglassing?  I saw a couple videos that showed the perfect alinement of the kayak halves.  Because they fit perfectly before fiberglassing, I expected a perfect fit too.

I have filets on either end and I think they contributed to the narrowing, or perhaps they just prevented the ends from returning to their original shape. I don't know what shear clamps are (although I could guess,) so I can't help there. I have tape on the inside and outside joining the hull and deck and two coats of fiberglass on the outside of my hull. My kayak is a few pounds heavier than I wanted, but I'm going to be taking it out into the ocean off of the Ventura area where weather is fickle, so I want a strong hull. My kayak is together and curing now. It's been a learning process.

Good luck.