As stated earlier, to set up an admin character, then you go to the flhook console on the system running the server and type in 'setadmin {playername} superadmin' (minus the quotes) to set your admin character up.
In order to change the messages that display ingame when you login (and on regular occassions), you'll need to go to your discovery install folder (In XP it'll be something like 'C:\Documents and Settings\Administrator\Local Settings\Application Data\Discovery Freelancer 4.88.1\EXE\flhook_plugins' - and the simple way is to run the executable in that folder called "playercntlsetup.exe" - just give it time to load all the data - especially if you have an older system first. Once that's up & running you can modify pretty much what you want in there.
Further modifications beyond that probably aren't recommended until you become comfortable with changing the other config files manually.