I went with #3. I mostly focus on taking the extra stuff out of the title (if it's a series, then that's for the series column, etc), and simplifying the tags. Hyphen Reader lets you change the cover in-app, so I leave that to do in there if for whatever reason I can't get the cover to change in Calibre. I don't mess with the files themselves otherwise.
As for organizing... Calibre - Read (Checkmark for Yes), Published, Title, Author(s), Rating, Tags, Series, and color coding. I went all in on customizing the Calibre UI to the point that I use a custom font and icon set.
