Thanks for sharing your template. I am sure I will learn something.
I use to publish both in PDF 9x12 and odt format. You can find one of these books on MobileRead ("Wellington's army", or "Mémoires du maréchal Suchet" among others).
Like you, I am not epub-fluent....
So my comments later..
Well, your text is pretty clear and very readable. I prefer b to a for paragraph indents.
Here are the main differences (just a matter of choice) with my template.
I chose not to use any header or footer because of the smaller screen template.
I like to add an hypertext TOC and a cover image (or some images)
I do not use colour for endnotes.
I like to use hyphenation and justification (small screeen again)