Thanks again everyone for the advice. I am almost out of the woods. Lots of sanding, and one round of fairing on the worst spots and all is almost well. I have a couple spots that need another round of fairing, and then I'll be moving on to the joining the next planks. As mentioned, these first joints will all be under glass and painted, so it shouldn't be a big deal other than time served. I have learned a bit about epoxy, sanding, and fairing.
To recap for anyone who may want to avoid fiding themselves in a similar situation, what I did wrong was:
1) Not dry fiting the parts to make sure they would lay flush. I beat the snot out of the stern bottom panel with a rubber mallet but two of the puzzle tabs would not lay flat even when the rest of the joint was flush. I should have taken the joint apart and removed all of the epoxy I had applied to the mating surfaces and fixed the problem, but I thought it would be within sanding range. Not so. When it was fully cured, it was worse than it was before hand. The unlevel surface created a space between the joint and the plastic for epoxy to pool on the bottom side.
2) I used too much epoxy. My main concern was to fully coat the mating surfaces, thinking I would scrape the excess off after the joint was set. Now that I know about the CA glue method, I might have wanted to use it since these first joints will all be glassed on both sides.
3) I may have mixed the batch too thick. It was difficult to coat the mating surfaces without making a mess. I will try a slightly thinner mix, and will use a smaller, more precise brush to put the epoxy where it belongs and not all over the place.
4) I was rushing. I had it in my head that the epoxy wouldn't last long in the cup before going off, so I needed to work fast. In the future I will err toward wasting epoxy instead of messy joints.
In the end, it all should turn out ok. Most of the joints may even look fine once glassed. The stern bottom joint will have visible fairing compound. I bought a 16" sanding board which will get a lot of use regardless of whether or not I bugger up anymore joints. I have an extra quart of micro balloons on hand now, too, as well as a heat gun. Speaking of that, I never was able to loosen the worst joint with heat. It was the bottom panel, so maybe the thicker ply and larger surface area wouldn't take the heat rapidly enough? I didn't want to burn the wood, and I just could not get it to budge. The best I could do was scrape of the excess epoxy, which was helpful.
The next joints will go much better. Even though they will have paint, I'm going to treat them as if they will be visible.