Thing is, vanilla THNs sometimes are structured quite vaguely and there is no system or pattern by which the different entity types are sorted throughout the file. Also, bases are usually made up of multiple THNs, so you would have something like one for the markers, one for animations, one with the actual props in it etc.
Anyway, you do not need to have the player’s ship in a THN in the first place. Menu backgrounds, for instance, are THN based, too, but there is no reference to any player ship at all. So in your base THNs you want to look for an entity that is obviously referring to the player ship and see that it rather refers to some object that you want to use as your shuttle instead.
If you happen to have a THN decoder or SDK, it doesn’t take a lot to read through them and learn to understand them. When I learned them, the tutorials were either unavailable to me or very old and insufficient. You still might want to have a look at our download section and our Lancer’s Reactor archive. There should be at least enough to get you started 😉
Good luck!