Instead of Sigil you may use MsWord (with
macros) . On outline view you can easily determine chapters. And you can also use the other ordinary tools of MsWord to format the text. (pagebreak, etc also possible)
PDF -> MobiPocket -> HTML -> MsWord (with macros)-> filtered HTML-> zipped filtered HTML -> Calibre (Toc according to h1,h2,h3) -> AZW3 -> Kindle PW.
Alternativley this way also possible though not used myself :
PDF -> MobiPocket -> HTML -> MsWord-> DOCX -> Calibre (Toc according to h1,h2,h3) -> AZW3 -> Kindle PW.