Having Formatting Issues in Calibre

Hello all, I wasn't sure which subforum to post in, but I'd appreciate some assistance after two days of trying things with no success.

I have a large ebook file I am trying to split into 3 parts. I've split one of my ebooks before with no issues. The problem is that my ebook seems to import into calibre with the background images too small for the text, or perhaps the text is not formatted properly.

However, when I open this same epub in Readium (a chrome extension) it is formatted perfectly.

How do I get my epub to format properly so I can split it with my epub split plugin and not have it jacked up beyond readability?

I noticed that when I am in the code editor, the preview shows the book just fine, but when I read the book in calibre, its malformed like in the picture below. What am I doing wrong?

http://imgur.com/a/9wxPJ