It's not uncommon that you will have a gap like what your picture shows.

based on your picture, it looks like your deck is flat (like it is suppoed to be).  so at this point, trying to force it down would bend the deck....which you don't want to do.

there are a couple ways to address this gap...which needs to be filled.  if the gap is relatively small which it appears to be, you can go from the rear hatch opening and put a piece of duct tape against the bulkhead/deck to close the gap temporarily.  then from the cockpit you can come in with dookie schmutz and fillet the gap.  when it hardens, pull the duct tape off and repeat the fillet process from the other side.   if the gap cannot be bridged by the fillet, you can cut a piece scrap okoume ply that fits the gap and epoxy it into place.  (and then fillet as normal).  

looks like very neat workmanship....keep up the good work.

h

   There is no gap too big to be filled by sufficiently thickened epoxy.

I'm into the 3rd wd double and each one has 1/4-1/2" gaps under the decks.