The history of "aikijujutsu" is very curious itself. One of the best books written on the subject is being released in a 2nd, revised edition (this week I think) - 'Hidden in Plain Sight' by Ellis Amdur; who is a member here and can answer far better than I can.
Essentially the term Aikijujutsu is proprietary to Daito ryu - which is very much (in terms of it's history) a Bagua-esque art. It emerged in the early 1900's, being taught by a single, enigmatic man named Takeda Sokaku. He was known to be a ... unique character, hyper paranoid, exceedingly violent. He had killed a couple of labourers following the Meiji era sword ban (and was almost killed himself by all accounts) when a group of them taunted him for still wearing a sword (he was better known as a sword expert at the time). Allegedly the judge told him that the era of the sword was done, and he should learn to adapt. He began teaching his 'previously secret' style of jujutsu - which went through several name changes before settling on Daito ryu. He was also the teacher of the founder of Aikido, Morihei Ueshiba.
The story he espoused about DR being a 900 year old art is about as likely as ZSF creating TJQ... and the man he credited with teaching him is not known to have been a martial artist.. which leaves the real history and creation of the art open for examination - hence Mr Amdur's book, which the original edition did wonderfully.
Takeda was known to teach different people different things. One of his students was a large, powerful sumo practitioner - Takeda informed him that he would teach him jujutsu (ie the mechanical techniques - taolu and applications, I suppose, in CMA terms) - to other, smaller students he said he would teach 'aiki' (which has as many definitions as there are teachers of DR/Aikido/HKD - but is often thought of as 'internal' goodies - jibengong perhaps, in CMA terms). The process of teaching or acquiring 'aiki' was/is reminiscent in many was of CIMA, and shiko is one of the integral tanren exercises (AFAIK - I'm not a DR guy)
In short - no-one knows, but it may be that DR was created/compiled by Takeda from disparate teachings. His father was a well known Sumo champion, and he was known to have competed (against his father's wishes) when younger. He also studied several other Japanese MA, some of which were known for 'unusual' conditioning exercises.
Check out the book if you're really interested - it's really very well done.