Also, I don't know what you are trying to do with the audio as LPCM streams inside of MKV should work if you have an appropriate player.
Let me understand you want an MKV file with WAV incorporated as a stream correct? What will you be using for playback? The reason I guess I am confused is the choice of WAV as opposed to FLAC and such.
Must all your software reside with MAC or do you have access to Windows? There are a few software tools that work in Windows but don't have a Mac counterpart that may help you.
If I am missing something here, please give some details and I'll try to respond with a more useful answer.