If the apex of the bow, the center of the top of the transom, and the apex of the lower, aft tip of the skeg all line up in the same vertical plane, then I don't see how the boat could be seriously asymetrical.  You should be able to check that by setting the boat up on a couple of horses, carefully leveling it side to side (use a level--you can't trust your eyes that way), and then sighting down from astern with some sort of plumb line (no need to get fancy--alarge fishing sinker on a string will do).

If it isn't seriously twisted out of plumb, you might be able to lessen the visual effect by re-shaping the top of the transom.  Looks like the transom of this design protrudes quite a bit above the gun'l's and the quarter knees, so you might be able to get away with that.

Hope it ain't too whopperjawed....

.....Michael

   Thanks, I'll give that a try.  To my eye, the bulkheads appear to be perfectly aligned with each other, so hopefully the problem isn't as big as I think it might be. 

If it only looks a little off from a certain angle to your understandably hyper-critial eye, then I would consider it a success, get over it and move on to enjoying the crap out of what you've built...

Aye aye Captain Skully! Yes I will enjoy it. I'm a little off myself, so it matches my personality.