I once pursued a memex solution like you describe and found that a simple static website generator worked well, but was high friction. You had to format notes, move files around, link images, etc.
My experience was that the collection of knowledge didn't produce many valuable insights or actionable results on it's own. I often found myself hoarding information, and creating a large backlog of things to process.
Summarization, linking, and contextualization are valuable, but then you have to do something to make that effort worthwhile, something that adds value to your life.
The more difficult part of this toolchain for me, was actually slowing down and thinking deeply about problems and connections. This required a disciplined habit of writing in a distraction-free environment (offline).
Once I realized the value of slowing things down, developing habits of reading (paper) books, and spending several hours a week writing and thinking, this diminished the value of having a fully featured knowledge tool chain for me.
I keep text files in a simple directory structure, and use cmd+t and project search in Sublime Text to find things.
That said, I'm still interested in a solution to this problem, since I spent no small amount of time is search of the grail.