I've advocated Gary Klein's work here before (Deliberate Practice for Decision Making ), you may find his latest book Streetlights and Shadows interesting.

The problem is that procedures are a system that describes how to react, but the model of reality that those procedures are based on is incomplete and may be contradictory (see Gödel's Incompleteness Theorem, though I may be generalizing it too much). The Drefus Model of Expertise lines up fairly well with your final questions, particularly the "Expert" stage. Unfortunately, it describe how one can develop that expertise or the answers to the questions.