Well the cleaning shouldn't be too tough. Flush it with lots of fresh water and for some of the really hard salt creep spots some vinegar should do the trick. Rinse again with more fresh water. The bio balls really can't be ruined much, they've already dried out after all. Just rinse with fresh water really wall and try to remove and junk thats built up on them and they should be ready to go.
Sorry I don't think I can really help you much with your plumbing problem. Can't really seem to wrap my head around the setup. Some pics might help, but to be honest I've never really been so great at that aspect of filter setup.