I can't seem to edit my post, I wanted to update before anyone here spent time replying.
I may have found a way to pull this off. I found a utility on Linux called "pdf2htmlex" and got a brilliant, near-perfect HTML conversion out of it. Maybe this can help someone else in the future.
I am now converting the HTML to EPUB in Calibre to see if that works better (I assume it should). I will post again with screenshots again once it finishes and report back - taking a very long time.
This is how the HTML conversion came out with pdf2htmlex: