None of those issues is the fault of AZW3 by itself.
The book has code issues that probably need to be addressed via the editor.
Conversion works best on clean (appearance) code
The reason Mobi
seems to work is because it is limited in what it could do and you
lost that poorly coded feature during conversion.
Basic HTML (what is inside an AZW3 and EPUB) is really not hard. Open the AZW3 with the Calibre editor, find the TEXT area that is giving you fits, then look at the CSS with the STYLES that were used there. Most attributes are pretty self explaining. Getting the
best values is the hardest part.