For linking, the tools I mentioned use [[Wiki Links]] - depending on which tool you use and how you do it, it’s either really polished or a bit clumsy (Foam is still alpha, so it’s a bit clumsy, but I love that I can use VS Code and my standard tooling to work with it, so I’m bearing with it for now).
Any of those tools would work with simple text files - they are basically text editors with specific features to support linking and visualizing your link graphs. Markdown is probably required to some degree to support linking, although I just tried out Zettlr and it treats .txt files as markdown.
If I were starting out, I’d try out Zettlr to get ideas about how a full-featured Research-oriented editor works, and then either stick with it or steal ideas from there into your personal workflow. I took ideas from Zettlr (like having a reading complexity score in the corner) and added it to Foam (which is really just a Visual Studio Code workspace customzed for note taking). You could probably adopt the same ideas with Vim using the right tools.