Can you elaborate on some of the issues you're having in the Chrome Remote Interface?
Yeah, D3 is what we're working with as well; also need to be able to embed the charts in Powerpoint, but that'll be a different story. All fun and games.
You can use inkscape’s CLI interface to get SVG from pdf, and then manipulate that with any XML editing library automatically
It works very well, but there are some gotchas with regard to the Chrome Remoting Interface.