Good, let us know the answer when you've done it.
The problem is of course easier if you make the scope narrower, for example if you know the two files conform to the same schema and you are only looking for differences in data content, or if you have ID attributes that you can use as comparison anchors.
Michael Kay
http://www.saxonica.com/
Author, XSLT Programmer's Reference and XPath 2.0 Programmer's Reference