I think this is a great topic...but I'm not sure it is something we can 'talk about' online..I think that finding a teacher who sees the body in this way...could open this up .. and make it come alive...as you suggest.
I think the phrase 'wisdom of the body', 'wisdom of the shoulder', etc...comes from CMA, not so much Aikido... right?
Sometimes you stumble upon interesting reads .. like for the hips/kua
I liked that site. Also; Joseph Chen's vids online may be of interest to you...he talks about mechanics and mechanisms of the body.
But ... this is not Aikido related. I don't necessarily know of a teacher who teaches like that. I would like to though..
Personally; thinking that one possible approach on how to learn more about this yourself...is to try to perfect any problem in your body....and/or physio websites; learning all the things that can go wrong...."corrective exercises", and their rationale...another approach is 'listening inside'...another .... finding 'biomechanically perfect movement', whatever the heck that is...(i.e. no grinding of the joints,.....no power leakage...optimal power transfer.. or a feeling of the 'body in suspension' (to steal a phrase)...internal balance held perfectly....a 'lightness'...and no slouching obviously..). learning from others' mistakes..
one example, i learned about; wrt 'The Big Toe' is due to the so-called windlass mechanism of the foot and fascial lines... and it's possible malfunctions
this is waaay big; but here is an interesting read; here<
...in this case the guy started to learn about the wisdom of the big toe, by finding out what the heck happens when the big toe stiffens' up ...and has limited movement. i found it interesting. maybe for you it is like watching paint drying.
just some ideas for ya.