I'm having the same issue getting the panels to fit in the notches 

Have you finished tightening all the wires yet? If not, that could be the source of the problem. As you tighten them (gradually and repetitively), the joints between the laps will close up a little. That might well pull everything into alignment. I've just about finished building my Dory and that's the way it seemed to work for me.

   Agreed with the above, plus this:  Panel alignment at the bow means equal overlap at transom for each panel.  This took a lot of fitting and adding stitches.  Note that no stitches wrap around the back of the panels implying the stitches are supposed to go around the back of the panels.  The predrilled holes from CLC are one each in the panel and transom.  I drilled an extra hole in the panel for each stitch goes thru the panel so that the stitch pulls the panel into position correctly.  Each stitch enters and exits the side panel, doesn't wrap around the back of the panel 

���Thanks everyone. We took a break for while since we were frustrated and then took another look. We just kept adjusting, added wires and tightened the wires up. You were right, it helped. Thanks! My internet was down and couldn't respond.

���Now we have noticed that the bottom is bowed. Both the stern and now curve up from the center. Is this nornal?

Yes. The stern has a bit of rocker, too. You'll be attaching the skeg to the back part of the bottom panel later, and the skeg will fit into this curve, thus helping your boat track well in the water.   

���I wrote that wrong. What I meant was that the bottom of the whole boat is curved. From the center to bow, and from the center to stern. It rocks slightly when pressure is applied. Sorry for tje confussion.

I believe this is suppposed to be there.  As mentioned above it is called rocker.  It is present on many kayaks and other small boats.

I don't really know whether the bottom panel should be perfectly flat after the boat is wired together. For most of us, at that point the boat is resting on a pair of sawhorses so we would never notice a slight rocker in the bottom panel. But I can't see any harm it would do . . . and it could be intended.   

   If you take a look at the line drawing of the profile of the boat, you'll see what we mean about the boat's rocker and the way the skeg fills in the curve:

http://www.clcboats.com/shop/boats/wooden-sailboat-kits/northeaster-dory-rowing-sailing-kit.html

Is there any curve to the bottom panel toward the bow? I'm not sure, but I don't believe there is much noticeabnle curve there.

I hope this helps reassure you.