Basically, it is just as HarryT said. There is no method of getting reliable, clean conversions from PDF to anything else, other than paper.
You may find your best option is:
- convert from PDF to an editable format using your best setting
- edit the result to fix the many leftover flaws.
- convert the edited document from #2 to your final format.
In this case you could convert PDF>EPUB, edit the ePub in calibre's Editor to manually fix the remaining flaws, and then convert the edited ePub to MOBI.