A description of what I\'m going to accomplish:
I know this questions is related to python but you could take a look 3DM - XML 3-way Merging and Differencing Tool (default implementation in java) but here is the actual paper describing the algorithm used http://www.cs.hut.fi/~ctl/3dm/thesis.pdf, and here is the link to the site.
Drawback to this is that you do have to cleanup the document and be able to pars it as XML.