I don't know how to go about it - currently it sounds a bit like a left wing Wikipedia. In my head, I can see it more like a giant 4D map, or a big messy case file sprawling out over a desk.

Well to butt in again, I don't know enough about it, but people here have said good things about Obsidian. This is the place I know of that shows how it might be used to build an interconnected knowledge base. I think it would be better for the kind of thing you're describing than a wiki would. There's no "4D map" but it does have a rotating 3D map of how different sections connect. Just a thought.