I'm working my way through Building a Second Brain by Tiago Forte. I can't say I've digested it well enough to recommend it, but a key point that stuck with me is to get into the habit of making a note of things you encounter day-to-day (including while reading and researching), and using the "PARA" method to file them into projects, resources, areas, or the Gmail-like "archive." Projects are things you're actively working on -- 2023 taxes, planning a night out for your anniversary, reaching a level of proficiency with LLMs, etc. Resources are a little longer-lived than projects; they're subjects you find interesting that don't have a clear start or finish the way a project does, like a bash cheatsheet, or a gardening hobby. Finally, an area is something that never goes away, like personal finances or family paperwork.
These groups have helped me organize my "lifestream" a lot better. Rather than torturing myself about deciding the perfect place for everything I learn, PARA helps me understand that organization is more of a lifecycle with stages over time. Something might go into a project folder today, but when that project is complete (or abandoned), its parts can go into reusable resources, mini-brain areas, or the archive. That fluidity has made filing of information a lot easier.
This isn't a full answer to your whole question. But knowing how to deal with the influx of daily information, and developing more of an opinion what a research session's work product should look like, is a piece of the puzzle.