I might suggest that you match both sides by reduing the bevels until they are even and re-do the bevel.  CLC kits are have close tolerences but you may be able to get by with the trim.  Short of that, you may need to contact CLC about possibly getting a couple replacement panels.  You have a lot of money invested in this project, so this may be a better choice for an optimal build. Good luck!

Welcome back to your build.

First, don't feel back because that is an easy mistake to make.  The Shearwater Double was my fourth build and I made the same mistake.  The SW Double has four hull panels on each side each with two puzzle joints.  I beveled the panels before assembling to length and when I got to that point, I had beveled the wrong side of one of the 32 hull panels.

1.  If your bevels are not overly agressive, the outer dimension/shape of the panel should be unaltered.  If that is the case, you should be able to go ahead and use the panel as is.  You will have to be careful to not pull the stitches too tight, which will keep the boat symmetrical.  You will end up with one seam that is a little wide but that is easily remidied with a bit larger filet.  This is what I did with my Double and all came out well.  There is one exterior seam that looks a little wider but I am the only one that can see it.

2.  If you do not like that approach, I would either make or buy a replacement for the damaged panel.  CLC is very helpfull and you will have a replacement in no time.

3.  I am not sure that I would recommend trimming the panel on the other side to match the damaged one.  The Wood Ducks use internal forms and bulkheads both in the hull and deck to hold the shape during construction.  You may have a hard time getting these to fit f the hull panels are altered too much.

The last point is that you are building a hand built kayak and not the space shuttle.  The boat will never be perfectly symmetrical and small variations are both expected and normal.  

have fun!

Before seeking or making a new panel, I'd try shaping and gluing a matching wedge to return the panel to its original shape, then cutting a new bevel on the correct side.