@OogieM The nice thing with Zotero and its plugins is that they are compatible in different operating systems, so there shouldn’t be any problems installing.
I’m not sure if it’s a core feature of Zotero or if Zotfile handles it, but dragging any PDFs to Zotero should extract its metadata (although 30 year old PDFs might not have it). You only really need the PDFs if you want to annotate them, so you could also just create regular Zotero items if that is enough for you.
I sometimes use my iPad to make handwritten annotations (It takes a little bit of effort to set up, but Zotfile manages this through your cloud of choice. See the section Sync PDFs with your iPad or Android tablet in Zotfile’s documentation. The only disadvantage there is that you won’t be able to extract handwritten annotations with Zotfile once at your computer, so I’d recommend annotating with a keyboard if you want to export them.
You can do this with the mdnotes plugin. See Zotero best practices - #57 by argentum for a small overview of what is possible. I haven’t tested with massive exports, but it should work for multiple items at a time if you select them with Ctrl+click.
At the moment the plugin doesn’t do it at the 1-highlight-1-file level, but you can do it at a coarser scale through colours (I also covered that a little bit here: Zotero best practices - #57 by argentum). If there are more people interested in having one highlight/annotation per file I could look into it, but off the top of my head the problem with that would be the naming of those files (unless we go Zettelkasten and use some unique ID for each).
Feel free to reach out if you run into any problems!