I thought it might be helpful to give an idea of the main PC programs that I'm using now. (I've ignored programs used for unrelated purposes.)
Some aren't in frequent use, but are an essential part of the system.
It's a very different system to the one I I had when I started this thread. Evernote and OneNote are out.
Some programs have databases, but everything is saved regularly into individual files. The main programs are cross-platform and I have them synced on all devices.
It's organised with inputs at the top, outputs on the right, and supporting programs below.

Mindomo is very new, and might not work out, but it fits a clear gap in my system previously tackled with a range of disconnected approaches - a successful bodge job but not the smoothest for workflow or efficiency.
I used it to do the diagram. All floating topics, which is why they don't line up properly. Multitudes of templates and themes, but none quite fitted. I did look at doing a simple change, but quickly learned how detailed and technical some of the configurations were. Will take me a long time to learn those and I'm determined to spend most of my time producing something rather than just learning, so it will be a long journey, even assuming I stay on the path.
Always possible I have forgotten a number of important parts of the system.