Is there any thought about presenting the papers as TEI XML with XSLT to display the paper in a browser or screenreader? TEI provides pagination support (needed for citing page numbers, because most of academia still needs that) and extensive semantic markup for things like bibliographic information. It also serves as one data model that can be converted easily with existing tools (XSLT) to provide many representations for humans, while also serving as a machine-parsable text for datamining. Digital humanities has made heavy use of TEI for years, and this project seems like it could benefit from it.
