The links in the book are configured to open in new windows. Unfortunately, this concept is foreign to PDFs. If you're reading the PDF in a stand-alone PDF viewer that doesn't mangle links (see Why do I get a 404 above), clicking on a link will launch a new tab/window in your browser.

However, if you're already reading the PDF in a browser, clicked links will open in your current window. This is a PDF thing. We can't fix it.

Solution? When reading the PDF in your browser, use the alt menu to open links in a new tab/window yourself.

— Amazon Issues: —

Why doesn’t that beautiful book cover appear on my Kindle?

Arg, Amazon. Their readers ignore the covers on books not bought from Amazon. Complain here.

Solution? Some folks solve this problem by loading their books onto their Kindles with Calibre.

Install Calibre 4.17 or later.
Attach your Kindle via usb.
Use 'Add books' to add your mobi book to the Calibre library.
Use 'Send book to device -> send to main memory' to copy it to your Kindle.
Eject the Kindle.

You'll see the book's cover appear, and then instantly disappear. Don't dismay.

While Calibre is still running:

Unplug and then replug the usb cable connecting to your Kindle.
Wait until Calibre sees the device.
Eject it.

Your book cover should again be visible. That is...at least until Amazon does something new to break this. Complain here.

How can I make a better version of the mobi?

You own your Kindle, but Amazon owns the software to make books for it. The license for that software prohibits its use to create ebooks that will be sold anywhere other than at Amazon.com. I suspect I don't need to say this again, but... complain here.

I'm not allowed to use Amazon's tools, but you can, as long the result is for your own personal use. Thus you can:

download our epub, and
use Amazon's Kindle Previewer to convert it to a mobi for your own personal use.