That would explain why you don't see the original items in-game. You have a .git that refers to items that you didn't extract, and while they'll show up in the module editor, the files to support them aren't present and so cannot be added to the .mod file.
You need to use the right-click menu on module to get the Extract for module editing menu item, then use that to extract. This will ensure that you're extracting what you want and removing any references in the .git for those things that you do not.
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