Here is how to do it so it comes out correctly...
1. Use Calibre to convert the PDF to ePub (do not use the delete blank lines option ever).
2. Use Sigil to edit the resulting ePub.
3. A/B compare the PDF to the ePub (every letter, every space, every punctuation, everything)
4. Edit the ePub to fix the errors.
5. Edit the ePub to fix the formatting.
6. Validate the ePub using FlightCrew.
7. Convert to AZW3 using Calibre.
To do this right takes a lot of work.