A while ago I used GOTSent for the MKV to XBOX 360 "conversion", but I switched to vista x64, where it doesn't work. So I made myself a tool that uses other existing tools to do this.
It uses MKVextract to get both streams.
Then it changes the h264level to 4.1 (really fast, just rewrites some bytes)
After that I convert the audio to stereo acc, using a tool that makes a wav and then the nero encoder to encode to ACC.
And at the end it is all merged together in a MP4 container with MP4Box.
if the file is larger than 4GB it is split and two (or more) output files are created.
It is as simple as it gets, choose input file, output folder and click convert.
If someone wants to try it out:
http://rapidshare.com/files/87075009...-0.1b.zip.html
But keep in mind, that is really a early stage build.