It's been burning in my mind all day: you're right that too often, for reasons likely hidden in the folds of of educational reform, some of our most powerful methods of working, researching, and writing are lost or seem like magic when they're rediscovered. Rarely are classes on the subject taught, thereby leaving the student to find their own way in the dark. Thank you for pulling back the curtain covering the proverbial proscenium arch on Act I of research methods.

For those flailing in the dark, Keith Thomas's brief essay (2010) discusses some of the basic problem along with solutions, while Adler and Van Doren (1972) talk about the levels of reading which are now rarely taught or reached (and how to reach them), and finally, imminent scholars/researchers like Umberto Eco or Jacques Barzun & Henry Graff reveal alternate versions of what you're already doing. Others certainly exist, often in piecemeal form, but this short set in combination with your YouTube channel for examples provides one royal road to the destination many seek.

• Thomas, Keith. “Diary: Working Methods.” London Review of Books, June 10, 2010.
• Adler, Mortimer J., and Charles Van Doren. How to Read a Book: The Classical Guide to Intelligent Reading. Revised and Updated edition. 1940. Reprint, Touchstone, 2011.
• Eco, Umberto. How to Write a Thesis. Translated by Caterina Mongiat Farina and Geoff Farina. 1977. Reprint, Cambridge, MA: MIT Press, 2015.
• Barzun, Jacques, and Henry F. Graff. The Modern Researcher. New York, Harcourt, Brace, 1957.

https://www.youtube.com/watch?v=SYj1jneBUQo

Forrest Perry shows part of his note taking and idea development process in his hybrid digital-analog zettelkasten practice. He's read a book and written down some brief fleeting notes on an index card. He then chooses a few key ideas he wants to expand upon, finds the physical index card he's going to link his new idea to, then reviews the relevant portion of the book and writes a draft of a card in his notebook. Once satisfied with it, he transfers his draft from his notebook into Obsidian (ostensibly for search and as a digital back up) where he may also be refining the note further. Finally he writes a final draft of his "permanent" (my framing, not his) note on a physical index card, numbers it with respect to his earlier card, and then (presumably) installs it into his card collection.

In comparison to my own practice, it seems like he's spending a lot of time after-the-fact in reviewing over the original material to write and rewrite an awful lot of material for what seems (at least to me—and perhaps some of it is as a result of lack of interest in the proximal topic), not much substance. For things like this that I've got more direct interest in, I'll usually have a more direct (written) conversation with the text and work out more of the details while reading directly. This saves me from re-contextualizing the author's original words and arguments while I'm making my arguments and writing against the substrate of the author's thoughts. Putting this work in up front is often more productive at least for areas of direct interest. I would suspect that in Perry's case, he was generally interested in the book, but it doesn't impinge on his immediate areas of research and he only got three or four solid ideas out of it as opposed to a dozen or so.

The level of one's conversation with the text will obviously depend on their interest and goals, a topic which is relatively well laid out by Adler & Van Doren (1940).

Forrest Perry shows an example of one of his zettels which has evidence of his having renumbered at least one card.

The image of the card has a strip of white out tape in the upper right hand corner with about 6 characters' worth of text covered over and the identifier "4b" written in black ink over it.

This will be much more interesting given that he'd first written about this topic in 1908 and has accumulated more experience since then.

Look for suggestions about the potential change in practice over the ensuing years.

Is the original version extant in his papers?