It's a great start to question these assumptions. For instance, if reality is objective but our perception is subjective, how can our perceptions really be about reality? How can something subjective be about something objective? And on the other hand, how did something subjective arise within something objective?

If we separate between epistemology (what we can know) and ontology (what there ultimately is) we can make the following distinction (from John Searle): conscious perception is ontologically subjective (it is a thing that ultimately exists in a subjective way) but epistemologically objective (we can study it like we study anything else).

I am fascinated by Hintikka's "Interrogative Model of Inquiry,"which goes like you describe of being an active sort of questioning, rather than going straight into analysis. It fits beautifully I think with the spirit of Judea Pearl's interventionist theory of causality

Try skimming through these two:

Hintikka, "Is Logic They Key to All Good Reasoning?"
Judea Pearl, "The Art and Science of Cause and Effect"