I would suggest clamp them back together and use a block plan to get the matching.  Very odd that, thinking that perhaps something shifted during cutting or possibly your jigsaw blade was on a bit of an angle.  regardless the get the two panels matching, otherwise you risk having a twist.

The advise I recieved was that you should build your boat to the centre line, as in make it symetical.

P.S. the block plane is your best friend when it comes to getting those little ridges and valleys smoothed out so that you have a nice even seam.  Once I cut out my WD12 panels, I put the plans away and worekd them to each other.  you will have a little variation and a beautiful boat!

I could clamp the 2 together and use the plane and make them match each other, but they wouldn't match the plan anymore. I'm talking an 1/8". Is that acceptable?

An eight of an inch is acceptable unless your WD is going into a museum.  Clamp the panels together on a flat surface and make each edge fair.  That means the panel edge should have a smooth curve from bow to stern.  Don't go hog wild with the plane, a little difference between the top and bottom pieces you are trying to shape is better than trying to make an absolutely beautiful new curve.  The curved shapes of the panels' edges are what make up your neat 3-D hull.  A small difference in overall curved edges is much better than a jagged or unfair edge.  Good luck.

Much more important than the 1/8 inch, is that they are lined up exactly before you start twisting the bow and stern. Once you twist them the panel pull together tightly making them hard to realign. Also you might still need to wedge/sand the bottom to get a smooth curve from bow to stern.

2nd the reclamp and block plane. much smoother than the jigsaw. Plane all of the panels, 1/2 hour now will save you 2-3 hours later.