So do I john. It is probably my biggest problem building kayaks - getting the deck/hull alignment. I am still looking for ways to cure this problem. I mark every form location on the deck/hull before removing them. I keep spacers at every location to hold the dimensions while glassing both sides. Once the glass is dry the spacers go right back in. I even install bulkheads in the deck while the spacers are in just to hold the shape. I keep spacers in both halfs as long as I possibly can and still I have this problem.
On my second boat, a Guillemot L, I did not use these spacers. By the time I was ready to mate the halves they were over an 1" out. I tried to slowly squeeze them back together over a period of 4-5 weeks until I finally split the bow of the deck with to much pressure. I burned the boat as I was tired of wasting my time thinking I could save it :(
Like everything in life this is just a learning experience - I just haven't learned yet :((

On another note, my wife is finishing cooking a big dinner as we speak for the last of our Holiday company. A few days to clean up the mess - take down the tree, etc. and she will be on the WCP site asking questions. I have been following your discussion concerning camping permits, etc. Kinda depressing - - - -