Dissertation research, twenty-first century style

One of the two main draws for doing an MSc was the opportunity to do an extended research project.  My program requires a 10,000 word dissertation on an original historical topic and I've picked the UK government's response to Israel's 1980 de jure annexation of East Jerusalem contrary to all international law, and formalising a state of affairs that had existed de facto since the end of the Six Day War in 1967.  My research centres around British government documents from the time at the National Archives, and contemporary broadsheet and academic journal writing.  The biggest problem I seem to be facing is how to organise that much information, but the lovely folk at Sciplore have written a tutorial on how to use open source software to manage not only your references but your notes and structure as well.

So my workflow looks like this:

• Track possible sources in Open Office spreadsheet
• For every source I make notes on, create an Open Office document with one page per page reference from the original source.  So if I'm taking notes on pages 5, 90-100 and 253 I will have three pages in my Open Office document.  Save this as an OO file, then export it to PDF (in a different folder).
• Open the PDF in Foxit Reader and add a bookmark with a meaningful name to every page of the PDF (which is why different pages for different page references mattered in the last step).
• Use Sciplore MindMap's monitoring function to automatically import PDFs and their bookmarks, giving me ready made notes of key facts and thoughts, complete with hyperlinks back to the notes I've taken.  For journal articles or digital pictures of original documents I can also use Foxit's comment feature as well as bookmarks.
• Rearrange nodes within Sciplore into a sensible structure, still retaining the hyperlinks.
• Update my spreadsheet with the source's status (to read / first cut / finished / useless)

Theoretically, JabRef will pull references data from Sciplore and then link back into Open Office to manage citations and styles.  I haven't tested this bit of the workflow yet though...