In case you may be interested in this, it's sort of a mess as I feel like I read a good line of research/methods, dash off in that direction, just to find a then-better line of research methods, running at a slightly divergent angle from the current point. Looking over my shoulder at the original idea, I feel orthogonal. Blame the word on all the article-reading.
At first I was highlighting then copying relevant passages into a word document, but it rapidly became hard to organize and find cites. So now I've stepped back and am utilizing the note feature of Zotero
with tagging. Now I can do full-text searches on notes and pdfs, or browse by thematic tags for different things, like "mongolia analogous" or "organizational culture".
The only problem is that this is a multi-step, tedious process - I read the PDF, highlight relevant bits, go back, copy and paste the relevant bits into a text editor, run a regex pattern I set up to remove extra hard returns and hyphenation due to papers' two-column justified layouts, copy to individual notes, then tag. Being a tad perfectionist, I guess - or just liking to gratuitously use regular expressions. It sure would be nice if I could directly edit those PDFs with Zotero and grab notes automatically, leaving only tagging to do by hand.
I suspect it wouldn't be so bad if I didn't know all the tools and regex bits, but it's definitely helping out. I think I'm going to do this for scholarly stuff I'm reading in general as it's a super useful writing aid. At least Zotero grabs the citation information first off (for most items) so I don't have to do that, and its citation plugin for Openoffice means I don't really have to pause mid-thought to write out all those little references.
Still, my current count for papers read and annotated in this manner is...63. And I have about 15 new things I found today to read. Ugh. I assume at some point I can stop reading and finally settle into doing.
If this is dissertation practice, I can't imagine ever being up for it.