Sounds like a job for Adobe Audition to me! If you can do it at all that is. I'm not convinced, personally, that speeding up the sound, i.e. changing the sound frequencies can be done without the change in pitch.
Depending on what you're tryign to achieve, have you tried disconnecting the sound from the video, speeding up the video and leaving the sound running at normal speed.
As for skipping silent pieces of audio... Presumably you want to simply take out the silect bits, moving the 'noisy' bits closer together. Once unclipped from the video, just treat it like any other piece of video, cut and splice it all over the place.
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