Threading Done
I think I’ve got comment threading working to my satisfaction. I ended up using YATCP, and I was quite happy with the flexibility of it. The only problem I had was that it’s stylesheet was included after the main one, so I had to either edit the one in the plugin folder (which could be overwritten on upgrades) or add !important to every line of CSS. I opted for the former because it was easier for now, but I might look at a better solution for the future. I’ll have to look into how I can change the include order of stylesheets in WordPress; I remember having the same problem before with a different plugin.
I cleaned up some style issues with the rest of the site as well, and added syntax highlighting.
Next Phase: Private Posts