Yup, I think you've got it. Just re-create in a separate folder the folder structure that shows in the sh3 progfiles structure, starting with the "data" folder. So your mod, let's say it's called ModX ... make a separate folder called ModX. It will have a subfolder called data, and from there you have to create subfolders the same as the sh3 progfiles structure leading to the various files that are in the mod. Then you copy over your ModX folder to the Mods folder under sh3. Then activate via jsgme.
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