>So while we can image, we can't know what correlates with a high degree of certainty.
I don't think I agree just on this piece, though you are making important points here. We can know, for instance, of visual or spacial awareness, reactions to certain stimuli or objects introduced in their environment, and so on.
You're not wrong on the importance of learning from active brain functions but I think we can at least make meaningful inroads with animals.
> Finding those foundational ideas and basic operating principles
I know a lot of people talk this way about brains and consciousness, that we need to first have our definitional elements before we proceed with research. But I think we often have, as the object of research, closing in on those elements, while gathering all kinds of functional and theoretical data from the mass of complicated noise that is brain structure and activity. We can build out correlations, mechanisms, and so on and close in on foundational elements.
It may even be the case that foundational organizing principles turn our understanding inside out in important ways, but I have never understood the idea that we are stuck if we can't start with such things in hand.