The video is easy - if you're using an AviSynth script, just add AssumeFPS("film"). This will cause the video to play at the correct speed without changing any frames.
You could also use AudioDub() to add the audio for your sync check. There's also a great filter that adds the audio waveform over the top of the video to assist with this process, I'll post back when I remember its name.
Edit - AudioGraph
To mux final video and audio together into the MKV container use mkvmerge.