Eek.
Yes, it can all seem a bit complicated, but it isn't necessarily. There were several Kuki-related branches in existence
before Takamatsu sensei's time, and none of them are "ninjutsu"
per se. . .though some contain elements of what people today would think of as ninjutsu such as strategies/methods for fortress penetration, disguise, etc. As has been mentioned before, a lot of samurai ryuha contained some aspects of ninjutsu; it just wasn't "what they were all about".
The only three purely-ninja systems in The Booj are Togakure ryu, Gyokushin ryu, and Kumogakure ryu. . .which is not to say, however, that they are the only ones that historically were connected with ninja. According to our tradition, two others -- Gyokko ryu and Koto ryu -- were originally Chinese temple fighting systems which were brought into Japan and went through generations of adaptation to local conditions before being picked up by Momochi Sandayu, a historically famous ninja leader, in the 1540s and becoming "ninja fighting systems".
Other than the three purely ninja-associated systems I mentioned, I'm not aware of any schools calling themselves ninjutsu/ninjitsu which have been able to prove a connection with any actual
old martial ryu in Japan, ninja or otherwise.
I guess I should start with some basic japanese terms as well.
Whats a Kan?
Whats a Ryu?
How does a "Family" relate to the Kan's and Ryu's (and what's that called)?
I'll let Don address that one, as he can give both a better linguistic overview and also perhaps some of the historical, social, military, and political implications.
You might find this biographical sketch and timeline of Takamatsu sensei's life interesting: http://www.ninpo.be/Takamatsu%20(eng).htm
