(I don't think the attempt at inserting a picture worked.) Anyway the problem is that as I suspected the puzzle joints on the bottom Skerry hull panel did not align very well vertically (strake joints are fine). I used a 2x6 clamping board screwed down very tightly with weights in the middle of the board. I suspect what happened is that, even though the screws were placed very close to the panel, their pressure may have caused the board to curve upward slightly and the weights could not overcome this. If I ever build another boat of this type I will put spacers the same width as the panels under the board and outside the screws.
At any rate my plan, because I do not want to sand too deeply into the ply, is to fill in the gaps on the worst side with epoxy paste and sand smooth. The other side looks pretty good. I will make the side with the filled gaps the outside of the hull, since I plan to paint the outside. If I decide to bright finish the inside it should look fine.
If anyone has a better idea, please let me know.