First, I want to say thanks for posting such a thorough walk-through of your experience with zettelkasten. I ended up using it as a sort of check against my own research and it proved very useful.
It seems zettelkasten, atomic notes, and inter-linking have become popular in the note-taking world, but I haven't seen many (any?) apps/tech that support both webs and trees, as you say here. So, I made a jekyll template that does that. I am still working on it, there's lots to add, the code isn't open quite yet, but I'd love to get feedback from anyone who is interested.
+1 for this response. I particularly like the blurry-to-sharp nugget, to which I wanted to add:
"low-res-breath > high-res-depth"