Looks good. I think you are going in a good direction. You could put something in between the 2 connectors and use some bigger shrink tubing go around both 5.5 connectors to tie the both together structurally. It would also be good for protecting the bare ends of the 5.5 cons.

If you still want to use the case you might have to remove the connectors all together and maybe just use 2 sets of wire. One for the batteries and one for the caps, providing you can get both sets of wire to fit through the case.