I've built one WD-12 and two Ducklings, and am now working on a third Duckling for another grandson. I each case, the most problematical part has been torturing the plywood at the bow and stern, especially the stern, to get them closed without tearing out the holes where the wires go through. Here's the bow before trying to close it:

http://i43.tinypic.com/2wgaxow.jpg
So I had an idea:
I used quarter-inch threaded rod, fender washers, nuts and wingnuts to gradually and securely close the bow and stern. I drilled 5/16" holes to accommodate the quarter-inch rod (to allow the rod to pass through at the angle) an d I used 5/16 i.d. fender washers for the same reason.

http://i42.tinypic.com/6f7687.jpg
Here's the stern, ready to see if the transom fits:


http://i39.tinypic.com/9ktdfc.jpg
And the answer:

http://i44.tinypic.com/2nquzr5.jpg

Perfect!
By the way, it helps to spray those parts with water before bending, as suggested in the manual.
You might wonder: what am I going to do with those holes? The holes closest to the sheer will ultimately be drilled out to 5/8-inch to accommodate 1/2-inch pvc pipe for my rope handles. The holes lower down will be glassed and filled, and covered by the epoxy-graphite bottom coat that I plan to use.
A couple more suggestions to make life a little easier:
Use extra wire stitches on either side of the temporary forms and bulkhead. As you force the panels into contact with the forms, the seam between the panels tends to open up at these points. The extra wire stitches will keep the seam tightly closed. Also, as you squeeze the bow and stern closed, seams nearby will want to open up. Use extra stitches there too, before closing the bow and stern.


http://i44.tinypic.com/2075bhw.jpg


http://i40.tinypic.com/2l8itty.jpg


http://i44.tinypic.com/30mtiko.jpg
Hope this makes your building experience a little easier!
Jim