The way to solve this is...
- Convert the PDF to ePub
- Use Sigil to edit the ePub
- A/B compare the PDF to the ePub and fix any errors
- Fix any formatting that is not correct
- When done with the PDF > ePub conversion, convert the ePub to your preferred format
- Load on your Kindle
- Enjoy reading
- Done
There is no way to do the conversion so it just works. And Mobipocket/KF8 are poor formats to convert to as you cannot then edit the resulting eBook. You do need to do an A/B conversion to make sure you don't have broken lines all over the place and other assorted errors. This is not an easy thing to do to do it right. The optimal solution is to just not bother.