Hmm, I wouldn't use medieval drop-caps in a modern text, but I guess it's a question of taste.

Other than that:

- the first page is top heavy. Very top heavy. Move the text down.
- The lack of paragraph breaks, however narrow, is somewhat surprising on an otherwise pretty empty page. Light is important.
- Avoid splitting words with dash in them. Just don't do that. Bumping "e-"in "e-reader" to second line is only marginally extend your spaces. And it's no 2-(4-Methoxyphenyl)-3-[4-(2-piperidin-1-ylethoxy)phenoxy]-1-benzothiophen-6-ol, either.
- Same applies to most particles and two-letter words. All "of"s "a"s and "is" are best positioned at the start of a line. Think of the speech rhythm. Put your breaks in the most likely places.
- I would completely exorcise the word breaks from the quote. You have tons of space at it's bottommost line, making an awkward hole in a block of text.
- The "triple dot" mark is often used to signal long break in dense texts; it's the semicolon of text structure, less important than a chapter but still bigger than paragraph. Personally I would push everything below it to the next page and make it disappear into the more natural break.
- I think you got your page ordering wrong. Page "1" should always be a right page. If you are typesetting for printing, the text should be moved to the right to allow for binding and inner margin. Hint: First three pages in this PDF should be right pages.

And finally..

.mobi and .ePub are going to destroy your careful formatting. Both format very explicitly reserve text flow to the final device, since the screen size, both in pixels and pixel density, is completely unpredictable. PDF is good format for that, in fact, possibly the best. There's of course .dvi, but you'll have problems finding people who know how to use it.

P.S. What software are you using for typesetting? Most good DTP packages have those rules built in, often with multiple templates ready to use.

I'm using LaTeX. Just LaTeX and vi. :P
So, No DTP software is being used. I'm diving into this kinda on the deep end of things so that I can more easily mess up and get feedback. Thanks, by the way!

For some of the things you mentioned (Specifically embedded Blackletter caps and the tipple dot) I know aren't appropriate, but I wanted to see if I could do them in the language.

I'll have to keep hyphenation breaks in mind, I explicitly have to tell the system not to line break at specific words, so It will just take a while for me to build a mental list of them.

I know that ePub and .mobi will reflow text, but I want to make sure that my workflow allows them to be generated if there is demand for them.

Let me touch up the document and see if I can produce a version that addresses the current shortcomings.

I could not figure out how to override the page numbering in any sort of clean looking way that didn't feel hackish as hell. I'll have to do more research.
Here is the resultant .pdf though: https://dl.dropboxusercontent.com/u.....ndInterest.pdf

The problem is that TeX is geared towards scientific publishing, not, shall we say, artistic one. Most of the points I made above don't really apply to a scientific or technical document but are important for the text that is to be read for enjoyment.

May I suggest trying out Scribus?

I prefer not to work with GUIs.

DTP is one of the situations where GUI makes more sense than anything else. I can't imagine doing proper balanced layouts without an interactive display or adjusting kerning in a write-compile-check loop.

Speaking of kerning, I think you should like this: http://type.method.ac/

I disagree respectfully. TeX has superior microtypogrophy control when compared to any graphical WYSIWYG DTP suite.