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The documentation for config.pasteFromWordCleanupFile here http://docs.cksource.com/ckeditor_api/symbols/CKEDITOR.config.html#.pasteFromWordCleanupFile is not exact.
Where it says:
CKEDITOR.config.pasteFromWordCleanupFile = 'custom';
should say:
CKEDITOR.config.pasteFromWordCleanupFile = 'plugins/pastefromword/filter/custom.js';
Also, IMHO would be useful to emphasize the fact that this setting can only be used on the global instance (CKEDITOR) and not on each instance.