All you have to do is to install a bookmark from the following page : http://a2k.aill.org/
You can choose between small, medium and large characters.
Simply drag the link of your choice to your bookmarks toolbar, then go to Aozora and search for a book.
For example, ドグラ・マグラ → http://www.aozora.gr.jp/cards/000096/card2093.html
Then, click on your bookmark (you don’t have to open the book). Kappa will be converted into a nice PDF file that fits perfectly into your Kindle.
After that, if you wish you can also find the mp3 files on the Internet (ドグラ・マグラ is free on iTunes) and save in on your Kindle, so you can listen while reading in the bus or in the train even if you don’t have your computer.