I'm confused. pdflrfwin, as its name implies, converts .pdfs to .lrfs, not .docs to .pdfs.
Anyway, you'd be better off converting the .doc to an .epub directly rather than using a .pdf as an intermediary. If you want to use calibre, use Word or OpenOffice to convert the .doc to an .rtf or .html file first. Or try one of the other tools around here, such as BookDesigner or BookCreator.
However, Sony Readers should support TOCs in PDFs if properly made. (Mine does, anyway.)
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