How tight are you making the "stitches" ?   One would think you'd make-up the whole boat connections loose, line the boat up and tighten the twists in the wire to get the right shape.

   also you might have to drill a few extra holes for additional stitches in the tough spots.  Its also good to have an extra set of hands to hold the panels in place, if you dont, you can rig up some straps to help bend them in.  Definately leave everything pretty loose until you have it all lined up and no twists in the hull.  then tighten your wires, check for twists again before you tack weld.

I found that when stitching my EP together that the closer I got to the end, the tougher it was to pull together to stitch because your lever arm gets shorter.  It was one of the only times other than flipping the boat that I needed help.

Of course, it's also very confusing when looking at the panels cut out to determine which is the top and bottom and which edges get stitched together.  I triple-checked mine and made sure to label my templates if I ever build another one.  

If the ends look like they line up sort of parallel to the transom and overhang by about the same, then it's a good indication that you've done something right.  

When you just look at the panels laying there loose, they all seem to curve the wrong way.  When you do the stitches, it all comes together.

Hope that helps.  Good luck!

Chris