I converted my story to Epub and Mobi today for my test audience and got them in the mail. I included my hand drawn version of the map as well! I hope you enjoy them, and find them well-formatted for your readers.
I believe I have solved the issue I was having with making the bookmarks work properly. I would appreciate it if all of you could let me know as soon as possible.
For all of the authors in the audience, I used Calibre on Linux in order to make the Epub and Mobi conversions. If anyone is interested in how this is done, or has a problem doing it, feel free to ask in a comment! It is fairly self explanatory for the most part, and the help section in Calibre is good.