The research manuscript example is exciting. It would be great if authors could link directly to the part of a paper that they are citing and be able to open that up if you want to dive deeper. Linking methods to results to discussion for specific experiments would make reading through dense papers a lot easier, and maybe have a notation/jargon definition section open at the same time. It's almost like a tiling window manager for reading.
I'm a little bit concerned about how it looks on smaller screens. It looks fine on my work monitor but I only have a netbook at home right now and a lot of websites have overlapping elements that keep me from reading articles. I haven't looked at this from that computer yet though. Maybe it would help to have collapsible columns if there are issues.
Good luck, I'm looking forward to seeing where this goes!