I would suggest setting up the bonus PDF as a separate product in Seller Admin, then you can have a "secret" page on your site (not linked from any public page) where you paste the Add to Cart button for that product, so you would publish the URL of that secret page in your book.
Buyers of the printed book would visit that page, Add to Cart the bonus product, and if it's priced at 0.00 (or you could provide a discount code in the book which reduces that product's price to 0.00), they would be able to use our Free Checkout method to provide their name/email and obtain their download link:
http://www.e-junkie.com/ej/free-checkout.htm
You could publish the file's password in the book, or just put it in the thank-you email we'd send each "buyer" of the free bonus book (keeping it more of a secret and allowing you to change the password occasionally). If you're using our PDF Stamping feature to deter file sharing, you could have the Stamper apply a password to each Stamped file, which could even be unique for each buyer's copy:
http://www.e-junkie.com/ej/selling-ebooks.htm
