Oh wow! An ancient FREDder! (A famous one too!)
If you want to be super thorough you could have a voice actor record all the auxiliary lines. But for just a single mission, I don't think people would mind too much if lines from different voice actors came seemingly from the same ship.
But FSOpen there are a few options you can use to silence a ship from making those type of messages (ship editor, misc button, disable built-in messages). I hope that's vanilla enough for you! (I'm not sure if by vanilla you mean no mediavps or no FSOpen)
Distributing any finished mod is best done with VPs, its just one file the user needs to worry about. You could create a VP with a single mission, a campaign file is not required for it to show up, even in a VP. But nothing stops you from making a single mission campaign anyway, with the new pilot file system, the game has no problem with one pilot file being used for multiple campaigns, even ones that have modded ships.
I'm not sure what you mean about your last question. Are you looking for some automatic way to time messages? That doesn't really exist, I'm afraid. It's all manual input for things like that.
And I'm curious, which mission of yours got included on the Sci-Fi Sim of the Year Edition?