I built two Chesapeakes and the bulkhead fit was a little bit of a problem with both.  It really does not matter what you do as long as you get a good mechanical/water tight bond between the bulkhead and the deck.  For smaller gaps, you can just fill them with "peanut butter" when you filet.  You can fill the larger gaps that way too but it might be lighter/cheaper to use a bit of scrap plywood on top the bulkhed as you describe.  I would keep the plywood strip narrow so that it does not interfere with the filet.  One tio that may help is to run plastic packing tape along the seam on one side of the bulkhead.  This will prevent the peanut butter from ozzing through too much when you filet the other side.  Once the filet hardens a bit, remove the tape and filet the second side.

I built two Chesapeakes and the bulkhead fit was a little bit of a problem with both.  It really does not matter what you do as long as you get a good mechanical/water tight bond between the bulkhead and the deck.  For smaller gaps, you can just fill them with "peanut butter" when you filet.  You can fill the larger gaps that way too but it might be lighter/cheaper to use a bit of scrap plywood on top the bulkhed as you describe.  I would keep the plywood strip narrow so that it does not interfere with the filet.  One tio that may help is to run plastic packing tape along the seam on one side of the bulkhead.  This will prevent the peanut butter from ozzing through too much when you filet the other side.  Once the filet hardens a bit, remove the tape and filet the second side.

i would second mark's notes above.  i have built several CLC Chesapeakes and all of them had a gap similar to what you described.   

my favorite technique is also described by mark....tape the gap closed on one side with duct tape, then come from the other side and fillet.  when the fillet has hardened , pull the tape off that side side and fillet the unfillted side.

my only other recommendation, is before you put the deck on, seal the top of the bulkheads (the open plys) with unthickened epoxy.  while the thickened fillet should accomplish this, since the fillet is thickened....its not great for actually sealing/waterproofing the end grain of the wood.   unthickened epoxy will do this easily.

h

   I think I added a piece sistered to the bulkhead to extend it to the template arc.  However I also got the deck curve a little higher than the hatch cover wanted so don't get carried away. The tape and filler might work better. Make it thick enough mix as to not drip all out.

   Thanks for the suggestions but I must be having a bit of a brain freeze here.  I assume the packing tape approach with fillet is to be done before the deck goes on - otherwise the far forward and aft sides of the bulkheads wouldn't be reachable.  However, without the deck, what am I applying the fillet to - unless I use a piece of scrap on top of the bulkhead?  And, just out of curiosity, if I had a perfect fit would the fillet be superfluous?  Thanks again

You fillet the bulkhead/deck joint after you cut the hatch openings (p135 of the manual).  You are going to love doing the fillet on the front of the forward bulkhead through the small forward hatch.  Luckily, no one will ever see it.