Use mkvtomp4 to extract all the tracks you need. As they write, “mkvtomp4 … uses mpeg4ip or GPAC’s MP4Box, mkvtoolnix and ffmpeg to convert troublesome mkv files to mp4”.
I use MP4Box since it is available in portage on gentoo.
When the mp4-file is made, use subler to edit the tags, add artwork and subtitles.