Finally figured out how to transcode MTS format to something that YouTube will take. One of the big problems I had before was the audio-out-of-sync issue, and it has been solved after getting the latest development version of ffmpeg (from reading this post http://ubuntuforums.org/showthread.php?t=529871&page=2). I compiled with the --enable-pthread option and installed it in /usr/local, and created a quick bash script called 'my-encode' as follows:
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