To demux the streams
MKVextractGUI
To remux the ac3 and the H.264 streams in a "clean" mkv:
MKVMergeGUI
Make sure you enter the appropriate fps for the video stream.
If you use mediainfo the original mkv fps will propably be reported differently than what youd get if you play the H.264 stream and look at its properties.
For megui to do the best job possible id go with the stream info not the mkv info
(if we have the same source mkv will show 25.00 and the stream will show 27.03)
This way all the streams info needed for megui to encode proper are in place.
Or you could add the fps to the avisynth script itself:
DirectShowSource("video.mkv",fps=27.00)
More info:
http://avisynth.org/DirectShowSource
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