I can confirm that the sample is 24 fps. You can only change the video that way in tsmuxer. You will need to re-encode the audio. See my instructions earlier in the thread (not far back).
In answer to your question, there's no problem keeping both audio tracks.
I really think you are on a hiding to nothing spending all this time on the sample. Just bite the bullet and download the whole AVCHD - V or I. You know AotC isn't out yet, right? :-)