Try Heuristic processing and check Delete blank lines between paragraphs. It might work depending on how the epub is built for the extra spacing between paragraphs.
The problem is usually in the Style sheet of the epub. It can be edited more to your liking just explode the epub using Calibre then edit style sheet then click rebuild epub. If the problem is then fixed then convert to mobi.
As for the other issue. I can't tell how many indie ebooks or self publish back titles I have bought with many problems like this. Myself I usually convert the book to html and edit it in word then reconvert in Calibre to mobi. Or if you use Sigil you can use that to edit the epub.
My last issue was the author put all dialogue in blockquotes. That was fun to fix!
Unfortunately ebook coding is like snowflakes no two are alike. so you can't just make a template to fix formatting problems. It has to be done individually most of the time.
I do know with the Kindle that font tags can cause issues so I always remove them specially the +1 -1 Font size tags.
You're best bet is to familiarize yourself with basic html and css styles sheets.