- The Jyuubi was driven by Kaguya's will probably from her subconscious rather than directly. It was mentioned by both Hagoromo & Itachi that powerful people can be corrupted by their own sense of power and lack of faith in their comrades. Kaguya was a mother after all and didn't want to directly kill her sons but as she used the power more and more she became more corrupted by it and eventually her subconscious was shaped by this.
However the Jyuubi is the original Shinji tree morphed by Kaguya's will into the Jyuubi. The connection between the two is that she ate the fruit that grows on the tree. The significance of why the fruit grows at all is still not 100% clear but may be a very important revelation later.
- Also Kaguya's combat experience before eating the fruit would have been at an ordinary human level with no chakra. Once she became the Moon Rabbit Goddess or whatever you want to call it she had no rivals to challenge her new powers. This may not affect her sense of strategy or intelligence but it does limit her actual combat experience in the sense she had no rival to challenge and grow from. As they say adversity is the mother of invention.
Otherwise there would be no reason for Zetsu to be giving her strategy tips. Madara needs no tips he was forged in battle and is perfectly adept at it.
As far as Shinji/Jyuubi is concerned I think it is deeply connected to the entire planet and there is some kind of harmonious cycle of energy between the "Earth - Shinji - Living beings" that is not fully understood yet.