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All of that indicates that's there's absolutely nothing wrong with your NCX file now.
Are you sure InDesign is exporting an ePub3 document? As the errors are indicating, an html5 DOCTYPE would simply be '<!DOCTYPE html>'.
You mentioned Sigil as part of your workflow. You do know that you can't open, edit or save an ePub3 document with Sigil and have it actually stay an ePub3 document... right? I only ask because I can certainly see Sigil adding all those DOCTYPEs that the validator is barking about (depending on Sigil's clean source settings).
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