This is an interesting approach Matt. The difficult thing is converting everything over and saving it all. Are you doing this manually or programatically?
In the past couple of years, I’ve been bookmarking everything I want to read to my own website. When I highlight and annotate material I’m usually doing it with Hypothes.is which has some really fantastic UI and aggregation functionality and then using either their RSS or API methods to bring that material back to my website or other private digital notebooks where I own and control it.
I’ve been reading recently about a few people   who have been using Micropub in conjunction with Webhooks to pull in content from places like Pocket using IFTTT-type methods. I’ve yet to puzzle out some of the pieces, and in particular capturing canonical URLs so that I’m not worried about intermediary sources like Pocket or Instapaper going down or disappearing from the web.
Separately, but related, I’m curious Matt what you do for marginalia you may create in digital e-books via e-readers?