Hello Doom,
  I think you want to use the Remove party member function call, this and many others are in the nwscript.nss;  
 RemovePartyMember(int nNPC); 
 Since you don't know which Party members the player will have in the party at the time so to remove all possible ones you could use something like this;  
 void main()
 {
 RemovePartyMember(0); // Bastila
 RemovePartyMember(1); // Canderous
 RemovePartyMember(2); // Carth
 RemovePartyMember(3); // HK-47
 RemovePartyMember(4); // Jolee
 RemovePartyMember(5); // Juhani
 RemovePartyMember(6); // Mission
 RemovePartyMember(7); // T3-M4
 RemovePartyMember(8); // Zaalbar
 }  
 As far as setting the NPC's selectability you could try this function in your script; 
 SetNPCSelectability(int nNPC, int nSelectability); 
 As far as the Transit system for custom modules, this thread (
http://www.lucasforums.com/showthread.php?s=&threadid=140253) you might find useful. 
 I hope this helps! :D