Save what you have worked on thus far, but I would re-do SH3 and GWX, to be certain you use "fresh" files. S3D has a "Save file to New Mod..." and "Save file to existing mod..." function, and that is the route to go when trying to alter existing files in the game. Also, the way the game works, is to run off of the Save folder, which does not get updated by JSGME. Therefore, if you add a new ship, it is in the game folder, but NOT the Save folder. If you are not seeing your changes, delete the "C:\Users \UserName \Documents \SH3" folder, unless you've edited that with MultiSH3, and then maybe the proper ship hull / funnel change will show. However, it sounds more like you want to change the geometry of the hull, and for that, you need to export said hull to an obj file within S3d, then import or open said obj file in a 3D app, such as Blender or Wings3D, do your edits (properly, which can be quite involved), save the obj file, and then re-import it into S3D... it can get rather involved.
