I read that you should glass the inside as soon as possible after glassing the outside because the epoxy shrinks a bit as it cures. This can cause some pulling on your deck or hull. And if you have to leave your kayak for a while, it's recommended that you put the hull and deck back on the forms and wrap a bungee around to help maintain shape. The dryness of your wood and/or humidity might also be factors to consider. I was lucky to not have much deck/hull mismatch, but the environment in my living room is pretty well controlled...;-)

As a suggestion, how about making your bulkheads now? I would try to split the difference between the deck and hull and make a bulkhead that's a compromise. Maybe more on the side of spreading the hull since this is easier than pulling in the deck. Force them in, then wedge in other areas that need it. Put a slight notch on each bulkhead at the shear so you can thread the fiberglass tape through before epoxying the inner shear.

You can also tie with wire just like you did with your stitch-and-glues...

Dean