I'm about where Ian is on a Guillemot single as well. I'm also having similar problems. I've used string to mark the centerline on the top and side of the strongback, but I have at least one form that won't line up. If I want the waterlines, chine lines and form centerlines to match I'll have to lower one form well past its side centerline (the midpoint of the 2"x4" hole). My strongback isn't nearly that far out of line. I guess my question would be: what else could be wrong?
Also, once the bow is aligned and the stern is aligned, how do I align the stern with the bow while my reference lines are facing opposite directions? How close does all this alignment have to be? Exact? Close enough?

As frustrated as I'm sure I sound, I'm actually having a great time working through all these challenges. It really feels great to use my mind and my hands to create something of beauty (as well as function).

Thanks for the help, everyone; you are inspiring as well as informative!

Rob