After using the TiVo ToGo to download the file, you can make it into an mpeg either using graphedit, or with directshow dump, which is much easier.
Sometimes the videos can be edited with any program, and sometimes not. TMPGEnc is free and its mpeg tools help to merge and mux/demux, but unfortunately its clipping tool doesn't work with my problematic video. For that, MPEG2VCR worked for me, though I wouldn't particularly recommend it for general usage.
Alas, no one (free) tool could do all I want, but this combination of free software and demos served my purposes for this situation.
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