Check out this link.It may do what you want. http://www.videohelp.com/tools/MKVtoolnix 1.Install MKVtoolnix (it creates a desktop link to MKVmergegui). 2.Extract the files from MKVExtractgui to the same folder as (1) MKVExtractgui will demux an MKV file. MKVmergegui will remux the files.
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.
Bump what! I already gave you the answer. Drag/drop into mmg, untick the streams that you don't want and resave.
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. You really need to convert to aac.
