Hi u/1aguafresca - you can have a look at Zenreader (disclaimer, I am one of the developers!).
It comes with a library for managing downloaded PDFs/articles and their metadata. It has a PDF Reader specifically designed for making highlights/annotations. The tagging engine allows you to group documents or the highlights by tag - great for large research projects.
Also, might be useful for you, Zenreader has trello-like boards for organising documents, so that you can keep track of progress.
Would be great to have your thoughts on this and see if it meets your needs.
Hey, saw your post: this is a bit out of what you asked (the tools mentioned above), but I have been working on a tool that is just coming out of Beta, called Zenreader. We built it to overcome some of the note-taking and organisational issues with tools like the ones you asked about.
Would love your thoughts on this!