In the MusicXML community meeting we announced an Open Source MusicXML - Sanitizer, a tool to a tool to sanitize / unify / cleanup existing MusicXML-files.
We would love feedback on how this tool should work, that's the reason we are publishing this very rudimentary version. At this point the sanitizer can clean out beams that aren't starting/stopping correctly, add accidentals (using the 'default' method on this page: http://lilypond.org/doc/v2.12/Documentation/user/lilypond/Displaying-pitches#Automatic-accidentals, other methods will follow), correct chord note durations for sibelius files and convert words in dynamics (eg <words>mp</words>).
If you are interested on what we plan to add: https://github.com/neoScores/musicxmlsanitizer/issues?state=open
At this point you have to 'install' the sanitizer, when it's usable it will be a normal website.
Feel free to contribute
Start here: https://github.com/neoScores/musicxmlsanitizer/