Eyrie,
I can't say how practices like the kuji-in were passed down but i can tell you they are not the sole property of ninjutsu or any other martial art for that matter. They are practiced independently or in conjunction with various arts. The kuji-in are not a martial art technique but more a tool used by martial artists who saw the potential in their use. They can be likened to qigong in a small way. Very few arts support or promote the practice of this such as kuji-in even within ninjutsu circles. I can only think that they are passed on in the same manner qigong would be. Iím sure you already knew this though.

I've had little exposure to them personally and honestly have little desire to. You may want to hit up kutaki or the ninpo/ninjutsu section at ebudo. Now that i think about it the genbukan forums may be a better idea as they lean more toward the ninpo side of the house than the others do and may be more inclined to practice and discuss them.
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Enjoy life while you can, you never know when things will change.