You have nothing to worry about.  This is a common problem or challenge area on Wood Ducks.  Even the manual provided from CLC shows the problem.  There are other posts on here about the transom on the wood duck.  Judging from your facebook picture you should be able to proceed smartly and I would not remove the rear bulkhead. Go ahead and stitch up the hull pieces to bring them together.  Patience pays off as you can move the wood together gradually without causing undue stress or fractures.  When you are ready to bring the side to the transom it would match up at the top of the panels quite exactaly and you end up with the hull sides extending about 1/8 to 1/4 beyond the transom.  This overlap is cleared up with about 2 strokes of a plane later on.  I don't know how to post specific pics from my blog.  But look at these two posts and I think they will look familiar to you.  

http://channelingnoah.blogspot.com/

Post #9 from 12/21/15, pic 2 - Holy Crap what is going on with the transom?

Post #10 from 12/22/15 - Problem with transom solved with patience, after searching internert for this identical problem.

Hope this helps.

   Your blog is fantastic.  I wish I'd found it earlier.  My grandson and I shall be consulting it as we procede.  The styrofoam blocks for support and the addition of a temporary support piece across the bulkheads just makes sense.  Now for my problem ... You seem to have brought the ends together with plastic wrap.  Is that ordinary Saran Wrap or packaging tape or something else?  When you say you sprayed the wood with water, how wet did the wood get and how long did you wait before pulling the wood tighter? 

1: Somebody stole all of the "junk" out of your garage. Or, maybe I need to clean some junk out of mine.

2: Take the day off. You brain will relax, and also process what you have done so far, and start processing what is next. While all of that is happening, the temperature and humidity in your garage will fluctuate a bit, causing the wood to like its new shape better than it did yesterday.

3: Pat yourself on the back. 2 days work, with no experience, teaching your grandson. Great job so far.

4: You might need a few more stiches, a spreader stick, or a spray bottle with clean water. If you are breaking stitches in the same area (bow and stern are common), add a stich. If the side want to poke inside of the bottom, add a little spreader stick. I didn't need water with the WD14 or WD double, but if you need to, spray about 2 feet of the side and bottom panels, inside and out, and wipe down with a cloth. Wait about 10-15 minutes, gently push the panels together, and tighten the wires a little bit. Then wait 10-15 minutes more and repeat. Gentle and patience are the key works, Okoume doen't warn you that it is about to break, it just snaps.

Good luck, JRC

   Thanks to Jnjclark and to martymo.  After a lovely Easter day off, I think I Nate and I can get this transom in order tomorrow.  I figured out that I don't want to use packaging tape since that would rough up the wood surface.  I need stretch wrap, that ubiquitous product that sticks only to itself and is used to tie packages together.  I'll get a good roll of that and use it with a little spraying of the side panels to reachieve the v-shape needed for the transom.  Thanks JRC for the detailed explanation of spraying and tightening. I'll go very slowly.  Thanks also for suggesting a spreader stick.  That may come in handy here.

As for the garage ... Thanks for the compliment. Cabinets are full of tools.  Wood is hidden beneath our temorary work tables.  The cars are in the driveway accumulating pollen.  Everything else was cleared out for this project.  My wife is already wondering when she will get her garage back.

CMcP 

Looks like alot of progress this week. Now comes the fun part, filleting, taping, and inside glass. Good job so far.   

CMcP,

I was able to stretch out garage possession for a couple of years by building her a kayak, too. Eventually, though, I did have to give it back.

Enjoy your build. After 8 years I still have fond memories of mine.

Laszlo