Wow, that shuttle is TINY! That looks amazing! (I'm imagining a bunch of shuttles flying around a starbase in a mission file, how cool would that look?) Still haven't gotten to see a freighter yet.
I did discover one last problem, though. Since you don't have any Elite enemies, you can't play at difficulties higher than 2, if you're using Artmis 1.4 or higher. Copying in Thom's stock Elites fixed this problem, so you can just copy your ships and make a few of them elite, and you should be good to go.
I'm also surprised that you can name your ships "Destroyer", "Cruiser", "Battleship" instead of the normal names. That's really cool, because I prefer those designations to the stock ones for Trek use. Mind if I copy that usage in our mods?