a call to CLC or posting a picture of what you have should straigten this out quickly....but in the meantime, i have a lot of Chesapeake experience and will try to help.

there are two relatively large deck beams that would be in front of each cockpit opening and a final deck beam forward of the forward bulkhead that would be there to maintainin the curve on the deck.

if you look at the CLC website you can lookup the bill of material (see kit parts) for the CLC double and if you scroll through each of the photos in the construction gallery of the CLC double, you can actually see picture of the deckbeams  (note, they also show pictures in the construction gallery of regular single cockpit boats so its a bit confusing).  but like i said, the basic approach is a bulkhead behind each cockpit opening...and one in front of the legs and deckbeams in front of each cockpit opening and one in the foredeck area.

that said, and not sure when it occurred, they changed their kit contents and approach to how they manufactured deckbeams....and this will effect your bill of material and instructions....and i don't know if they ever synchronized these.  https://www.clcboats.com/shop/kit_options/chesapeake-double-tandem-kayak-kit/79.html

the older approach was a laminated deck beam....these were usually the larger deck beams.  and they were strips of wood glued to together and bent in a jig to the right curve.  they were very beefy becuase they needed to support the forward edge of the cockpit which gets a lot of stress.    after that they changed it to pieces that were cut to the right curve out of thicker okoume plywood and you were responsible for glueing them together/doubling them up.   the forward, smaller deck beam was never, in my recollection particular beefy and did not need to be (page 15 of the construction gallery) ..becuase it was just there to bow the deck up.....so this might explain the problem of the instructions vs the material you have.

anyway, i hope my description above helps.  you will get it sorted out.

h

   Hspira- Turns out we were missing a couple pieces! CLC just sent them our way. 
 

Additional questions:

- Chesapeake double has three deck beams, the center one is a different shape than the forward and aft beams. It also appears it is a different radius than the forward and aft beams, close to 1/2". Is this going to be a problem when fitting the deck? If I were to fix the deck to the shorter center beam, I'd end up with a dip in the middle of the deck. The center beam has notches on it to fit against the shear clamps, like the bulkheads do, if I were to sand down the shoulder of the notches, I'd be able to raise the center beam up to the height of the other two beams. Does that sound like a terrible idea? 
 

- The bulkheads stick out proud of the shear clamps pretty significantly, especially the aft one. It makes it a bit higher than the forward and aft deck beams. Again, we'd have deck laying issues like the shorter center beam described above. Should we plane down the tops of the bulkheads to be even with the deck beams?

CLC usually gets it right so please also check with them.  but let me see if i understand the question and at least offer some things to consider and you can follow-up with CLC.  pictures, are of course, useful.

if you are asking, from the middle deckbeam (the one at the front end of the forward cockpit), from that point forward, if the deck, will have a slight upward bend to the bow of the boat, the answer is yes.  and that is why you have the forward-most deck beam up there to make sure for the slight upward bend toward the bow, you still maintain a arch in the deck.  its a very subtle shaping....but that is how chesapeakes work.    so i would not sand down the notches to rather center deckbeam.   but based on your description you are saying you want to raise that forward bulkhead which in my thinking would increase the bend of the deck leading to the bow.....so i am not sure i understand the concern or maybe you need to help a bit more with the description.

on the bulkhead question, this needs to be sorted out.  my first question is did you ensure when you glued your sheer clamps onto the hull sides that you remember that the sheer clamps are supposed to be 1/4 inch (i think that's the dimension) proud of the sides..  the shear clamp is where the arch of the deck starts its upward trajectory to the bulkeads from the hull sides (note you have to plane the sheer clamp into the shape of the bulkhead..and that is why it needs to be proud of the side).  if you did not do that, that could explain why the bulkhead looks proud.  if you did do that, then something will need to be adjusted.  typically when i have had to adjust a pre-cut bulkhead that has a curve in it,  i have found it easier to cut the bottom shorter as its usually a straight cut/adjustment and easier that trying to re-shape a curve properly.  

https://www.clcboats.com/shoptips/building-stitch-and-glue-kayak/beginning-assembly-stitch-and-glue-kayak-video.html  at about minute 8 into the video shows what i am talking about with respect to sheer clamps proud of the hull sides.

hope that helps

h