I agree, Briss is the way to go.
Almost all of my PDF conversions needed some post processing as well. Here is my workflow:
1) Open in Briss and crop borders, headers, footers and page numbers. Save to new PDF.
2) Email and convert to AZW using my free Kindle email account.
3) Import to Calibre and convert to EPUB.
4) Open epub in Sigil to hand edit and tidy the book. Remove Calibre's title page. Build TOC.
5) Import again into Calibre, add meta-data and cover, reconvert to EPUB and then finally to MOBI ready to be loaded onto the Kindle.
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