The torpedo door sound is triggered when you press the keys to open and close the doors, so I don't think it can be changed. I could be wrong of course.
As for the "Yes, sir!" files, they can be changed to anything you like, as long as you have something that fits. Personally I just got tired of having the guy say "Yes, sir" just before he shouts "ALAAAARRM!". I just try not to look at his silent lip movements and ignore the resulting delays.
Sorry I couldn't help more.
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