Ueshiba now knew and Takeda didn't?
This is qualified just how?
Ultimately your post covers both sides pretty well. I just meant: Takeda didn't exactly spend time in a library studying the "classics," right? His life just wasn't like that. He grew up in pretty messed-up circumstances.
Whereas, Ueshiba really did grow up comfortable and reading this type of stuff.
Anyway I think the best evidence we have for the way info was organized in Takeda's mind (and what info was there, period) is as you say-- we have to look at the info in the extant branches and look at what is conserved across that diversity. It's still speculation, and the biggest problem is indeed:
how to separate what was not known from what was kept secret. Ultimately that could only be guessed at from body movement and usage.