Ninjitsu (Togakure Bunjikan dojo Taijitsu) is not an art, more of a way of life, and it is far from "dead". I must agree that it is dufficult to find a REAL instructor. However, Ed Martin and Bud Malstrom (in Georgia) are two individuals that I would recommend as contacts to find Bunjikan Dojo teachers. Stepehen Hayes has gone his own way with the "quest Center" view of classical Bunjikan teachings, in MY opinion. His teachings are more oriented toward todays modern world than the old scrolls of the Togakure lineage. Yet, he is a good place to start. One of my friends, a Shodan, is in Japan currently learning with Shirashi Sensei and Soke Hatsumi whenever he can. We learn from him what we can during his short visits back stateside. In the old Dojo we actually had Shirashi Sensei teach whenever he came stateside for buisness. It was only a handful of times but they were weekend crash courses from 8am to 10pm Fri/Sat/Sun.
as far as what is practiced tody you are correct about speculation, The only guide to the old ways is throught Hatsumi and the scrolls. Even then, there is subterfuge as to what is really being taught. In a classical sense the scrolls teach a list of technique, a Kata, to those so inclined to use the word. With each technique there are hanka (variations) depending on various factors. However, the core is the same; position, balance, timing, spacing, mindset all matter. Different schools within the system focus on differnt things, thus different Kata. In Gyokko Ryu a more circular system of unbalancing, striking, parrying, "blocking" are taught where in Shinden Fudo Ryu a more lineare approach is emphasised. In the Togakure Lineage there are 9 schools (ryu) and even then a few are specualtive at best as to what the underlying teaching is.