Organisation is a very personal thing - and your RSI etc. issues are obviously going to limit your choices.
Have you tried any wiki software? There are a few "personal wiki" items listed on
this Wikipedia page, and a Google search may find more. And at the bottom is a link to PIM software, some of which may offer helpful features.
For personal Wiki I tried WikiPad and Zim - but didn't like them much, and probably not quite sophisticated enough for what you are looking for.
Or you can search for Mind Map software - these don't float my boat (my mind is full of those places generally marked on maps as "here be dragons"), but maybe you can find something you like.
When evaluating, specifically look for the search features and check out how easy they are to use. It does not matter whether it's an outline, a wiki or mind map or what it is, there will always be stuff that gets misfiled or otherwise lands where not expected, so you need a good search facility. With a good search facility, good organisation becomes optional.
Of course, if your own mind is fairly well organised, just a simple folder structure in which you place your carefully named files can be good enough. I find it convenient too keep simple notes as plain text or HTML files, with only actual documentation in Word/LibreOffice/Whatever format. Then I use
Agent Ransack (for Windows, I presume Mac has something similar available) to find by name or content or date etc. It's super fast and easy. And, if you learn how to use regular expressions, it's also very powerful.