I think your problem has to do with epoxying, sanding, and re-epoxying, not varnishing. If what you're seeing is what I see in my Pygmy Arctic Tern kit, the light spots are due to sanding back down to wood and then re-applying epoxy. I had to re-do one of the butt joints on one of the lower hull panels (due to air bubbles under the fiberglass cloth strip) so I pulled it off, sanded it back down smooth (sanding completely thru the epoxy in some places) and re-did the butt joint. In the places where I had sanded back to wood, the epoxy turned out lighter. I am guessing that during the first attempt, some of the epoxy saturated deep into the first ply of wood, which sealed it. After sanding and re-applying, the second coat was prevented from soaking in as the first coat had done, and this accounts for the color variation.

Unfortunately, it's kind of late to fix it now -- and fixing it would require sanding it all the way down to wood. Your only consolation is that, despite a little variation in color, your boat is still nicer than any plastic or fiberglass one. I, too, got very critical of my work during this past winter's building process, but I've had the boat out in public a number of times (including a kayak symposium here in Michigan) and have recieved many, many compliments. By the time you get done, only you will know of these 'defects' -- John Q. Public will see your boat as a whole, and will say, "cool -- did you build it?!"

Deano