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Import your source to Word or LO Writer.
Properly style everything including different page styles, headers, footers etc.
Export/Save As PDF.
Calibre primarily converts ebook formats. You can produce PDFs from it, but that's limited. Sometimes "Printing" a PDF from the viewer works. That works as well as "printing" a web page to a "PDF printer". PDFs are WYSIWYG previews of paper print, or files to do paper printing, inc professional publishing, That's why trying to convert from PDF to anything is even worse. They are not ebooks.
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