I was building a skerry, albeit from a kit direct from CLC.

A similar issue came up but they came together with only the smallest gap that you can't tell now. by putting in the bulk heads it brought everything together.

That said, one of the new updates was that the bottom panel was also routered and it needed to face up rather than down like all the others. given the size and what not I wonder if this is the issue, or rather if it could be the solution.

another tip I have is to loosen up the wires, they should be tightened later, I had mine to tight at first and loosening them let the boat "settle" into place.

I am sure others more experienced than myself have better ideas as well.

   You've been very clear, and welcome to the fun and challenge of boat building.  Even with the precut kits that I've used from CLC, slight variations in the pieces of wood and dimensions create what is called "tolerance stack up"  that results in minor differences, even with perfect assembly technique.  Give that I'm far from perfect as a boatbuilder, I've had every one of my builds result in some mismatch at the far end from where I started stitching.  

One suggestion I would offer is to loosen the wire stitches a little, get the transom installed, then go from back to front, wiggling and moving the planks a little at a time to get them better aligned with each other and the transom.  It will never be perfect, but if one or two are overhanging by a centimeter, I would not be too worried.  Wait until you have it all tightened down and the first gluing done to trim the ends.

 If the overhang is symmetric, like if the same planks on each side have similar overhang, then I'd guess the hull is symmetric.  Use the manual instructions on how to determine if you have any twist in the hull before gluing things in place.  I'm assuming the Pram manual describes how to use "winding sticks" like the Skerry manual does.  If not, search for "winding" on this website for hints on finding and fixing twist in the hull.  Here's one page:  https://www.clcboats.com/shoptips/stitch_glue/checking_twist.html

Can someone tell me if the outwales are 2 or 4 per side ? It is not cleare in the planes...

Thank you very much

The Eastport Pram Sail is 39 Sq ft. or 42 Sq ft. ? or someone can pass the measurements of the four sides to be able to have it made correctly. Thanks   

 The sail is  39 sq ft. or 42 sq ft. ? Someone can pass the measurements of the four sides to be able to have it made correctly. Thanks for answer