You should be able to use mkvtoolnix to split both versions at the same time code, then load up the first chunk (crawl and opening shot) from v3 and append the second chunk (rest of the film) from v4.2 and render out a new MKV. That’s how I join films that are split across two discs (like the LOTR EE’s).
(The append part, not the split part - I think it splits along keyframes, so if your keyframes aren’t in the same spot there might be a problem with this method.)