The Google Diff, Match and Patch (https://code.google.com/p/google-diff-match-patch/) supplied me with the tools I needed. I quickly implemented a Java comparer which compare each file to the one I choose as a reference. I still have to look at four comparison results, but I ask only once the comparison and all the results are on the same page, making it easier to locate exceptions.
I must clean the code a little but will try to share it if anybody is interested.