Now is a good time.  Won't find an easier time.

I'm a newbie too, and only a step ahead of you in assembly. So take that in considering my advice. I also had some better looking joints than others. I sanded them smooth to help me decide which looked best for the outside of the boat before stitching.

You might try heating the puzzle joints with a heat gun, being careful to not char anything, and maybe the epoxy will soften enough to press the joints together.  If they won't go together you will have to sand them smooth, which will remove the thin top layer of wood, and use a painted finish.

Thanks for the input folks. I think I'll go ahead sand these down, even though it will slow things down for now- sounds like a winner in the long run.

I think its a good point that I'll then be able choose which side will face out vs in (planning to paint the outer hull).

Cheers, Hickory

Yes,I'd sand them smooth now, being careful not to sand through the surface veneer (been there, done that). After some sanding, if you have a lot of step between some of the joints, now is the time to try heating them to get them lined up better. Dave

I also had one puzzle joint that was not smooth.  I did not want to sand the wood with the resultant loss of a plywood surface veneer layer and discoloration.  Add a few thin layers of epoxy to level the joint out and fiil in the area, and then sand.  The resin is clear and makes the joint look perfect after sanding, and I now can not detect which joint is was that had the problem.