It's nice to have the plywood of a puzzle joint perfectly flat (if possible). If you mess up, you can do a little sanding but stop as soon as you see any evidence that you are close to sanding through the first layer of the plywood. If the joint still isn't level, you can fill the low side with a bit of thickened epoxy and then sand it smooth.

Don't worry about the fiberglass cloth on the inside. (1) It's probably not necessary at all. (2) It will only show in the cockpit and that doesn't need to be a thing of beauty (some roughness is helpful, being less slippery). And even in the cockpit those strips of glass will later be covered with a full layer of glass.

So, try your best to get the joints perfectly flat. If you fail, a little sanding is OK -- or you can use a great gun to take it apart and start over.

You have lots of options and lots of choices.

Thanks Birch2.  This is helpful.  I was wondering about using a heat gun and redoing it.  My thought was that I'd have to sand out the little bits of expoxy that remain on the edges of the puzzle joint and this would compromise the tightness of the fit.  But if that's not necessary I'd lean toward doing it again and clamping down the joint as it's curing.     

   As far as the manual being enough, the manual I used was good but I also used a book, videos, and this forum. Getting other ideas or seeing how someone else delt with a challange is often a good idea. There is more than one way to build a boat (or as the saying goes "more than one way to skin a cat" but I don't know who would skin a cat. This is why the forum exists.

Ralph

   Thanks for the input!  I gave it a light sanding this morning and the joints are almost perfectly flush to the touch, maybe a couple thousandths of an inch off in a few places - no veneer removed.  I'm going to assume those kinds of tolerances are alright.