The picture shows the joint before scraping excess epoxy. It also shows that the joint is not entirely flush along the entire length. I'm hoping it's good enough for a painted hull, given the subsequent epoxy and fiberglass steps. Not having done this before, I'm not sure what will be necessary to make unevenness "go away" in the finish.

For #1 panels, I will remove enough material to achieve a dry fit, and see if that goes better.

After scraping clean-up.

That's definitely good enough for a painted finish.  Some epoxy/woodflour putty forced into the gaps will take prevent voids under the glass. Go easy, though, because it's a bear to sand off. Just pack the gaps, squeegee it flush and when it's cured sand it smooth.

Since you're painting, you can use epoxy/phenolic microballon mix to both fill your weave and fair the boat. It's lighter, cheaper and easier to sand than unthickened epoxy. If you use a longboard to fair it you'll have the basis for a yacht quality finish.

Have fun,

Laszlo

   That looks better than the first puzzle joint on my skerry did!  You'll be fine.  What Laszlo said, fill, squeegee, sand, move on.  In fact, if the edges of the puzzle are all well mated with no serious gaps, and it's just a high/low, mismatch between the two halves, you can use the microballoon mix to fair that as well. It's not as strong as the structural mixes (wood flour, silica, or Cell-o-fill). I used the phenolic mix on the deck of my Kaholo, and of course painted it.  The phenolic fairing mix is purplish in color so it won't work under a clear finish.  It does sand out way faster than the wood flour putty or even straight epoxy.