So far, I've just come up with a list of officers that make sense given the ship's role. For a whole crew list, I would break down under each "department head" so to speak.
So a transport might have: Captain, XO, Chief Engineer, Navigator, Foreman, Communications, Pilot or even more. Really depends on how you envision the ship running and separate the duties, in addition to each ship.
As for scaling the ships according to equipment, this is an interesting idea. However, the scaling in freelancer seems off, comparing fighter cockpits to transport windows etcetera. Might still be an interesting experiment.