Now I understand why what you are doing won't work.
1. Never, ever add new files to the game's assets. Make a new .pk3 with your altered npcs.cfg or .npc extension files in a folder called ext_data.
2. That NPC tool you are using is for Jedi Academy only, not for Jedi Outcast. The best thing to do if you are making a new npc with the .npc extension is to copy and paste whatever type npc you want class-wise(Luke, Imperial, whatever) and paste it into Notepad or Wordpad and make any changes you want to it and save as (name).npc.
I hope everything I just said makes some sense. If you need an example of what I mean, I'll paste one into a reply.