I've never seen Skim, it was only that I recalled the exchange I had with piovac. I also have problems with multi-key shortcuts - it's one reason I like MS Ribbons, you only need one finger to drive them
Have you considered using Evernote for your projects.
- EN works best on Macs, i.e better than it does on Windows.
- It is good at organising loosely coupled information structures
- Evernote Premium has an integrated PDF annotation feature that works on embedded PDF's i.e. PDFs you drop into a note. Sample attached.
- You can copy a note-link from EN, paste it into a calibre custom column, then when you click it in the calibre book details pane the EN Note will open. No plugins or add-ons needed to do that.
BR