I really like the new PDF and the idea of pulling the various bits together into 1 package. Please take everything below with a huge amount of salt; I have 0 paid professional experience with publishing.
General Comments
I understand why you have the varying widths for the left margin (so that things look good if the document is printed) but I don't think too many people will be printing this out. It may be better to optimize for screen reading. If you do, then I'd suggest switching to a serif font and making the margins identical throughout. Then you can also get rid of the blank pages.
Part ___ Pages:
- I think you can omit the page numbers on these pages; it will look cleaner.
("Business Lesson 2:…") and other similar blurbs
- Since the text is a little too wide for a single line, maybe "Ever." should be indented to line up with "Don't ship stuff that blows up". That way, the phrase will look connected to "Don't ship stuff that blows up." rather than "Business Lesson 2".
Fun Facts/Interludes/Asides/Other Little Boxes:
I like how you set off the "Fun facts" . They're a nice break for the eyes. Since they float on their own, you can even get rid of the colon and just use "Fun Fact". The same goes for "Asides", especially since you already omit the colon for Interludes.
I also noticed that sometimes, there's a blank line under the box and other times (e.g. pages 42 and 91) there isn't. It should be consistent.
Links to other web pages:
- The light blue box is really jarring and seems to come from out of nowhere. Please keep it consistent with the way you do links in the Table of Contents.
- I see that some of the URLs are hyperlinks and some aren't. Consider making all of them links or all of them not links.
Page-specific nitpicking...
Cover page:
- Looks a little odd without an author/editor name.
Page 2:
- Wait, isn't this page 1? (Normally, cover pages aren't counted or, if they are, they're counted with tiny Roman numerals)
- It looks more like a forward, preface, or introduction; it was really strange to see the "2" up there.
Table of Contents:
- Great idea!
- Maybe you could make the text blue or underline it; the red boxes are a bit jarring and make it harder to read the chapter titles
Page 85:
- The whitespace between the 2 boxes can be trimmed down to 1 line break.
Page 231:
- Missing a line break between "Or take a long constitutional…" and "Why can't you take me…"