unzipped it to find out why, and discovered it was made with calibre. e-book developers hate that program because it does a rewrite of the underlying .html and .css files, creating an unholy mess that's very difficult to decipher. personally, i won't touch a calibre file; life is too short.
aside from the .epub, the .mobi and the .pdf do just fine in getting the content across, so even though i would likely have done them slightly differently, what you have is fine.
still, if you really want more feedback, i can give it. but the original markdown files would be best, concatenated so they're just one big file, with the text running linearly.
(a book really works best with the whole thing in one file, because that usually minimizes editorial inconsistencies while you're writing, and makes it easier to check later. it also dampens file-clutter considerably, which is good.)
-bowerbird
