You’re putting way too much effort into it. Most of the people preaching all these different things you “have” to do for “good” PKM are selling snake oil or organizing for the sake of organizing. It’s a new-age religion to them and it holds just as much water.
The simplest way to handle PKM is to build it over time, and do so naturally. That way, it’s something you know, that you recognize, and is personalized for you. That’s the most important part: it should be yours, not Johnny Come-lately from some infomercial on YouTube.
Tags are the easiest way to start, alongside links. Anything beyond this pushes into unnecessary, and often nonsensical, snake oil.
A quick-and-easy start is to limit your properties to two tags, one for the theme of the note and the second for the sub-theme. For example, #gaming and #rpg, or #literature and #mystery, or #photography and #nature.
If you find a unique or relevant word in your note, you can turn it into an inline tag, but that’s not necessary. This will start creating your network naturally and takes little extra effort.
Once you’re comfortable with tagging, if you know of a related note or expect you’ll create one eventually, you can link a relevant word to the related note, or even a non-existent note if you plan to do it later. Instead of going to that note to add a link to the new note, you can enable Backlinks (a core plugin) and the link back will be created naturally.
Don’t worry about metadata. Don’t worry about refactoring. Don’t go back over everything constantly to add links or tags or widgets or gadgets. Start small and easy, build your own process, and turn a deaf ear to the peddlers pushing “The Best PKM Methodologies” or “The ONLY Way to organize your notes” or whatever else. Give them the same attention you would a hustler on a street corner, because that’s all they are.
And yes, that includes me. They’re your notes. Do what feels natural with them. I’m just offering my take on PKM, just like everyone else.
If you absolutely, positively must go beyond tags and links, wait until handling a couple tags and the occasional relevant link is second nature.