There's nothing wrong in your modlist. Everything should be fine. I don't use GWX at the moment, so I can't compare your ships' dimensions to mine. Maybe some GWX player here in the forum can check their recognition tables and see if there is a difference between theirs and yours
Charts addon can't be installed through JSGME if one is not a GWX+Magui F user. It can be added through manual editing but that is such a big work that I doubt many people will try that.