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1. Turn off automatic metadata update in preferences under calibre integration. Though the namespaces are pefectly valid. It is epubcheck as usual that has its head up its arse.
2. Choose whatever name you want for the file, including directories when you are adding the file.
3. No you should not add that file to the manifest, calibre will warn you about such files since they are typically reader specific files that contain out of band information. It's up to you to either delete the file or ignore the warning, or add the file to the manifest, if possible.
4. It's absolutely pointless making toc.html if you already have toc.ncx. epub 3 supports toc.ncx, just use it.
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