No need to extract since mkvmerge handles mkv input just fine. In fact if your mkv contained native AVC (pretty likely) then you wouldn't be able to remux since mkvmerge requires mkv or mp4 input and mkvextract extracts raw streams.
Their are 3 audio languages, all in AC3 format.
1. German AC3 5.1
2. English AC3 5.1
3. Japanese AC3 5.1
I want to delete the Japanese and German languages/subtitles leaving only the english ones.
mp4 with AC3? Not part of the specs, although I do recall reading that Nero had plans to store AC3 as private streams, so it may be possible in the future. Still playback is an issue since any spec compliant solution wouldn't need to support it and would just ignore the stream.
