I had the same problem with a MC16.5 Hybrid That I built two years ago. 

CLC's reply was, "The culprit is the sheer clamps.  Made of solid timber, every single pair of sheer clamps has its own bending characteristics.  There will always be variation from our prototypes---a little more, a little less.  Every boat with sheer clamps is going to be shaped a little bit different in plan view.  The carlins, too.  This is harmless for the boatbuilding purposes, but molds might be a sloppy fit.  We try to get them as close to average as possible.

The purpose of the molds is to support the strip deck, temporarily.  They don't need to fit perfectly to fulfill their function.  Set up the molds so that they're more or less evenly spaced---you might need some small shims---and that will be perfect."

If you want pictures, let me know your email address and I will be glad to email them to you.    

Good Luck,

 Kodiak Jack

Thanks Kodiak Jack,

I thought that would be the case. All other measurements are fine. Sorry it took so long to reply, I've been sidetracked for awhile. getting back on it to try and finish by spring.

John