what files would i have to rename or change to fly different ships in the missions?

You would have to modify the Shiplist to say, if you want to fly the Outrider YT-2400, it would go from
!SPECIES_111!YT-2400,Shuttle/Light Transport,Nonflyable,Known,Skirmish,
to
!SPECIES_111!YT-2400,Shuttle/Light Transport,Flyable,Known,Skirmish,

I think that's all there is to it.

what about flying a x wing instead of a a wing in the single player game? changing what ship you fly in the missions

Don't you hate it when they answer something entirely different?

Download AlliED. (or other similar editor.)
Install.
Open each mission and select the fg you fly in (there is a braceted 1 somewhere, as in i player. I think it is always top of the list.) from the flight groups list. (You can use a pop up window to make all areas available.
Alter the craft, armaments, or head to options and fiddle around there.

i played through a level and gave myself crazy ships, and i blew up all the bad guys
i should off had like 60000 points, but it only counted 5000 points at the debriefing screen, and only kills for unmodified ships!

burnt hotdogs!