Ellis Amdur discusses the history of Isshin Ryu in his book Old School. He suggests that, while there is little evidence to conclude that Nen Ami Jion was the actual founder of Isshin Ryu, it would not have been uncommon for a ryu's founder to give credit to great past martial artists who lives had provided him with some degree of inspiration. Thus the actual founder of the ryu (Amdur names Tan Isshin, the sixth headmaster according to the official history) could have named a list of his personal "heroes" as the "spiritual" founders of the ryu, even though they had nothing to do with the actual techniques of the school.
Old School contains an excellent section on Nen Ryu as well as the chapter dealing with schools of kusarigama. If you want more information, that might be a great place to start. Also, there are several practitioners of Shindo Muso Ryu (the school that has retained Isshin Ryu's techniques) on this board who may be able to answer your questions regarding the history of Isshin Ryu. I don't know if any Nen Ryu practitioners actively post here, but I remember reading some posts by a Nen Ryu practitioner during a search through the archives. If you search for a while you might find a way to contact someone currently involved in that school.
David Sims
"Cuius testiculos habes, habeas cardia et cerebellum." - Terry Pratchet
My opinion is, in all likelihood, worth exactly what you are paying for it.