Grab a heat gun or a hair dryer and cook the epoxied puzzle joint.  If it hasn't been more than a day or two since you glued them, you can unstick the puzzle joint and glue it again.  

John, thanks for your advice.  The thing is, though, that I sanded one side, which looked fine, before turning the panel over and discovering the problem.  So now if I softened the epoxy and tried to straighten the joints some of the fingers would be too thin.  Live and learn!  Now I know to look at both sides before sanding.

I think my idea to put spacers on the outside of the screws to prevent the clamp board from bending is a pretty good one though.  The shorter boards on the strakes did not bend enough to cause any problems.  If I do see some bent fingers, though, I can use your advice to fix them.

By the way, here is a link to the picture: http://www.photoshop.com/users/DanaDCole/albums/0bd795f944c04d899d6931e5f7a28500

Boy, that sure looks familiar, you sure you weren't in my garage?  I don't think you have much of a problem as you have not sanded through the venieer so if you use very fine sand paper on a very flat piece of wood you may be able to take those epoxy puddles down some more.  Be sure to watch the edges of the puzzles because that's where the venieer will start to abrade the most at first.  Stop just before that happens.  If you used a filler in the epoxy to glue the joints, that will effect the color of the finish so the less of it there is, the better the finish will look.

Thanks Wing, good advice.  The joint looks good on the other side, so I will use the side you see in the picture for the outside of the hull, which I plan to paint.  That way I can use epoxy paste filler to smooth it out and the discoloration will be covered by paint--plus it will be on the bottom of the boat.  I might also try using silica instead of wood flour to make the paste so there will be less discoloration--what do you think?

The "good" side will be on the inside of the hull in case I decide on a birght finish inside.

Don't use silica or wood flour for that.  Wood flour is hard to sand and silica is harder yet.  Get some micro ballons, which are little tiny hollow glass balls, to use for filler where you are going to paint.  It's made for exactly that purpose and is much easier to fair.  It will come out a purple color so that's why you don't use it in any area that's not going to be painted.  You'll probably have more areas to fair prior to painting so it's good to have it on hand.

I had a similar problem with puzzle joints on the CH18. Before I realized how much of an alignment problem I had, I had sanded through the veneer on one of the hull sides (unfortunately facing out). So I'm going to do some kind of racing stripe over the side puzzles even though only one is kind of bad looking. Live and learn, but it should come out looking pretty good. They really do need to be clamped down firm and well aligned. My follow-on deck puzzle joint turned out a lot better. Next time, I will try the heat gun if the alignment looks sketchy. Dave

Thanks again "Wing" for your advice.  I will order the micro balloons right away. 

Thanks also to "Ludwigd."  I can tell you that the heat gun idea works very well.  I had a couple fingers on the rabbeted side that bent themselves out of alignment.  The binder clip idea in the manual does not work at all--gets in the way of proper clamping.  I didn't think about the forum, so wrote directly to CLC.  John replied and explained about the heat gun.

I suppose a hair dryer will work also, but I have a heat gun at work so borrowed it.  The epoxy doesn't just get soft and allow you to move the piece.  Instead it suddenly pops loose and then you can move the piece into place.  After that you can re-glue and clamp it perfectly.

Because I had such a tiny area to glue, I used regular epoxy (Gorilla brand, tan in color) rather than mixing up a batch of MAS.  I figure it will be sealed up in MAS epoxy later and will be painted so no worries about water infiltration or discoloration.  I hope this was not a mistake.

FYI, Shore...   I read an article about different glues and epoxies.  It was in a professional wood working publication I get and it stated that the one part glue...Tite-bond III (3) is as good, in most cases, as the two part epoxies.  PLUS, it is a tan color.   Food for thought when making repairs.   I have used Tite-Bond III in boating AND land based construction projects without having it ever fail.  I'm sold on the stiff for making wood-to-wood bonds AND MAS or West Systems can be applied over without a problem... ~BRUCE~ (Wood Duck 12..."DAFFY DUCK"...)  

Thanks for the info.  I'll look for that stuff!