Chris,

If what you are describing is primarily an alignment problem, the photo below shows my version of a wedge clamp that I saw on Kent LeBoutillier's web site. You hot glue the U-shaped portion of the clamp just below the edge of the hull shear and then slip the wedge into the opening, and it will align the joint.
I made up about 40 or so of these clamps and used them at one foot intervals. At the bow and stern I added a couple of extras so the interval there was more like 6 inchs. You can see additional photos of how the clamps are used at the link below.