let me see if i get this correct.. there is no gap at the TE but only a gap where the joiner is? Maybe the former on the wing root got warped or something..
I bet VF would have a good sugestion on that one.
Looking at the measurements you have taking of the gaps. Maybe the joiner isn't perfectly lined up in the wing core itself. If you try to push down on the wing what happends to the gap? If its equal on both wings I would say you could probally build up the wing root with some extra balsa to fill up the gap.
The first picture isn't really clear... but, do you think that the joiner on the right wing (male end) is to long and causing it to push the other wing out? Either way you look at the problem it looks like the joiners are not in far enough in the wing. Maybe some extra sanding in the wing core itself, so you could get the joiners to fit in tighter..