Muxing sound and video different sources

[bilbonvidia]

I have a HD vid MKV but the audio is in german. I managed to get hold of the video in english bus at a much lower quality visually but the sound is fine. I have managed demux both of these files. I am now trying to remux the english audio with the german film. The audio was extracted to a wav using vdub. The english video seems to be a few seconds longer though with added black after the credits. The credits on both videos end at exactly the same time though. I have tried converting the wav to aac and then mux to an mp4 using Yamb but the sound does not work. I think I need to chop the end of the audio off first so the time matches the video I am trying to mux it with. What is the best way for me to achieve joing the audio and video together decently?

[Baldrick]

I would extract the audio using mkvextractgui (requires mkvtoolnix), cut with audacity, export to mp3,aac and mux back to a mkv using mkvmerge.