There are several different lengths for shakuhachi, in order to reach higher or lower pitches. The default size is 1.8, standing for 1 shaku 8 sun (Japanese measure system similar to feet and inches, hence the name "shakuhachi": shaku for the measure and hachi, that means 8, for the 8 inches left) or 54,5 cm approximatedly. The default shakuhachi is toned in D (Re).
On the longer shakuhachi it is easier to play the higher octaves and on the shorter ones the lower notes are easier. The default size is good for learning the difference between octaves.
Good breathing can be acquired with time and training, or by other interesting means. For example, to learn minyo tunes, one also learns to sing the songs, not only to make a better instrumental part, but to know when to breath, and how long to hold. Almost every shakuhachi player can sing a little.
Another way is to control the blowing. For a good sound, is not a powerful breath that is needed, but rather a deep, wide breath for lower notes and an also deep, but thin breath for higher notes. The factors behind this are: steadiness, length and most important, lower body force, which leads to the third training:
If you're a martial artist, you probably have heard of the infamous horse stance. The horse stance is made by placing the feet wide and lowering your legs until the inner angle of the knees reach 90 degrees or so. The training is to breath in, and out slowly with force, while appling strength on the lower belly muscles (like when you're at work in the bathroom), whilst in horse stance. This greatly enhances your breath control ( and thigh muscles :-).
Applying force to the lower belly when blowing is the basic technique to sing, or to play any wind instrument.