For a start, Abbott's book is in Kinko notation, which, except for in Australia and Hawaii, is the most common notation used outside of Japan. I usually suggest learning Kinko notation before Tozan because of the important fact that the repertoire of pieces called honkyoku ('original' or 'main pieces' from the Zen Buddhist tradition) doesn't exist in Tozan notation.

Also, a variation of Kinko notation is used to notate honkyoku of other lineages (eg. my teacher Yokoyama's pieces and the Meian pieces). In addition, Abbott's book has a number of features that other teach yourself books don't have, such as a section on making one's own practice instruments and another section that graphically and effectively takes a beginner through his/her first honkyoku.

Carl's book comes with cassette tape and also has follow-on books for the really motivated self-taught person.

Carl also has a book for more advanced players, and one with well known western pieces. The latter is particularly useful in developing a sense of pitch while playing the shakuhachi.

People who already can read staff notation, can teach themselves to read western staff notation on their shakuhachi in a very short time with minimal effort. Beautiful music composed or arranged for the alto/tenor recorder is close to the 1.8 shaku length shakuhachi range. As recorder players know, there is no lack of that sort of music around!

If there were a teach yourself book in Chikuho notation, I'd recommend that one for reasons I won't go into here. But as there isn't, I recommend the Abbott book. Finally, once you are comfortable with one notation system, you'll probably want to learn other notation systems anyway, as there are great pieces unique to each system, including (I will grudgingly admit) Tozan! So in that sense, it doesn't really matter what system of notation you begin with.