I don't have any "documented" evidence handy, but I was told by my sensei (Seiki Ryu Kenjutsu/Jodo -- an Aiki-related art) that O-sensei had studied Kashima Shinto Ryu and "Yagyu Ryu" (he didn't specify Shinkage, Shingan, or both), and used those and his other koryu and gendai Budo experience as a foundation for his Aikiken & Aikijo.
He also told me that most of the early students of O-sensei had prior martial arts experience, and that their input was seen early on, as well.
Yours in Budo,
---Brian---