Taking a quick look at the file, it's a mess. If you have the original Amazon copy and it is KF8/azw3, I would suggest using KindleUnpack to recreate the epub file instead of using calibre to convert to epub. If it was mobi, you are kinda stuck with that mess.
Looking at items such as:
Code:
<div id="box1_1201" class="para-normal">
<span class="char-of-normal"><br class="calibre1"/>
</span>
</div>
generating a blank line where a simple <p>& # 160;</p> would have pretty much the same effect.
Not to mention the <br class="calibre1"> being used to break paragraphs which are not present in my copy of the ebook.