I’m glad to hear about Scalar and look forward to checking it out myself. I’m a bit surprised you hadn’t heard about Omeka. Their main site has some great examples of it in use which might help your investigations for examples. I recall seeing some interesting map-related projects by Anelise Shrout that used Omeka which you might appreciate for their interactivity.
Since you’ve got several sites on WordPress, you might appreciate potentially using it to provide some of the functionality you’re discussing.
For pop-ups on references you might appreciate the Academic Bloggers Toolkit plugin.
For highlights and potential feedback, you might take a look at Hypothesis which is an interesting highlighting and annotation tool. It allows private groups which a writer might share with an advising committee or even provide for public facing markup and sharing. There are available WordPress plugins for expanding functionality on one’s site, though the tool is a free-standing one.
I suspect that if you look around the plugin repositories for WordPress and Omeka, you’ll see a variety of plugins that can extend the functionality to do some of the things you’re interested in executing.