If it was a set of panels that I'd cut out of something cheap, like luan, I'd simply recut another set.

If it was a set of expensive panels, like precut ones from CLC or such, I'd try first to do some trimming with a little plane (works great, far better then sand paper). I would *not* try to get them to be perfect mirrors. This would remove a lot of wood. I would first get them simply closer, then I would mark with pencil on them both the differences between them. I would then attempt to adjust in my stitching process, and see if I could get the boat fair and symetrical this way.

If I could not get the boat fair because the differences in the panels caused to much asymetry, I would unstitch the boat, and make the panels equal, and then restitch. I would then examine the stitched hull shape and determine if it was adequate for my use in its now not quite as designed shape. If it was acceptable, I'd proceed on. If it was not, I'd then redo the panels.

I would sugest for future work that you cut and glue the panels one atop the other, using wax paper between them. Consider drilling holes at the edges of the panels to pin them together if needed. The little plastic tubes that come with spray cans make a dandy pinning agent.