An updated approach.
- Go to ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books.
- Once there, locate the 881256329 epub folder. You must use a non-beta version of the book. Beta versions are DRM’ed. If your version appears to be DRM’ed (a holdover from the beta period), delete it in iBooks and re-download.
- Copy this epub folder to your desktop. Remove the epub extension, zip it, rename to epub. Apple uses a non-standard epub format, and these steps transform the book back to something Calibre can import and convert.
- Drag this epub into Calibre.
- Click Convert books, choose PDF.
- In Page Setup, select default output profile, set margins to 72 on each side
- In PDF Output, add printable TOC.
- Click OK and let the conversion start