The Matched Pairs nodes demo'd at the last SIG meeting held at Vernalis in September have just been released. See http://tech.knime.org/book/vernalis-cheminformatics-nodes#MMPs for details, or install them (Version 1.3.0, available in KNIME v 2.10/2.11 and nightly build) and have a look. The nodes allow for multiple cuts, and for separation of the molecular fragmentation and pair generation stages.
Any questions or suggestions, please let us know either via the forum or by email to knime [at] vernalis [dot] com.
Steve