So when I was converting the book into the proper document style, I realized the final copy looked terrible for some reason on the kindle preview. I didn't know how this happened, but it had made a mess of the formatting. Luckily I have several versions of the book saved at all times.
What I found out is that there was a bunch of formatting changes I had implemented in the shorter version of the book which I had previously published on kindle, but I had not made those same changes to the long draft.
What this means is I have to re-indent every paragraph, re-break every chapter and re-align every section break.
Originally I had planned to have the book up today, but next Monday is now my target date for having the book up for sale. It'll be $2.99 on the kindle store. I'll keep everyone updated.