I’ve never done anything like what you are working on, but I’ll throw out my 2c in case it’s helpful. If I were approaching this problem, I’d be whiteboarding it in order to get a sense for how things should be organized and linked.
First I’d list out the categories, topics, and key concepts I want to capture. I’d put each item on a post it note so you can move it around the whiteboard. I’d then try grouping and linking them, and use a notation method that shows me if the links are sequential (a leads to b) or just related. Or should just be cross referenced.
You may not get an order of things you find is “perfect” from this (or maybe you will!), but at the very least, doing this kind of exercise should really help you understand how your info fits together.
It can also help to have a buddy who likes doing this kind of nerdy stuff to do the whiteboarding with. I always find the interaction and need to explain your thought processes to each other during this kind of work is very helpful.