You need to take a step back and form a picture of the overall structure of the ideas. Concretely, you might do that by clustering your scraps into piles and observing the structure that emerges. Or you might sketch a mind map or a visual outline.
Andy suggests taking a step back and clustering annotations into piles or using a mind map or visualisations to identify common themes.
I wonder if this is a bit overkill for the number of notes I tend to take or a sign that I'm not taking enough notes?
What tools are out there that could integrate with my stack and help me do this.