Additional comments - July 2009.
To change the starting ship or add in a new start, you change L\true\gamestarts.xml. This contains the basic start details, including the starting ship, and the details seen on the game start menu. New starts cannot use text file references, and must be hardcoded as text within the quotes of the gamestart statement. (only text in the 03.cat text files is referenced as the game starts, and this should not be touched.).
Each start included in gamestarts, needs to exist in 2 parts of director\start.xml.
The first part includes the plot activation.
The second part includes starting ship fittings, race relations, additional player ships and viewable sectors.
To add another ship, use the <create_ship command, at the same level as <reward_player. Example in the Yaki start.
WARNING : If you make the start.xml file too big, it may not execute on lower end or memory limited computers. I particularly found this when also adding a lot of stations and ships to the game using multiple setup.... scripts. Its like the computer makes a list of things to do, and start.xml and your setup scripts are well down the list, and if the computer runs out of resources, the start.xml just doesnt get done.
To get around this, if your start.xml is going to be large, then only have a single setup script, that checks for a global variable on starting the first time, and because it doesnt exist yet, it does nothing except turn the global variable on. After the first load of a save game, the setup finds the global variable exists, so calls your scripts for what you want created in the game. It then sets the global variable to something that says its completed, and all other times the game is started, it should find the task complete and so not run anything else. I recommend you include hotkey creation at the same time.