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If you're converting the PDFs to Word, then you could try using Word's semi-automated "Table of Contents" feature. You'd have to apply heading styles to the headings you want in the TOC, then, at the point you want the TOC, use the Insert - Table of Contents command. You want to set it to use the heading styles, to not include page numbers (unless you have reason to want those included), and to use hyperlinks. That'll generate a Table of Contents from the heading styles you applied.
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