First of all, with this method you won't be able to view your level in JK2 yet
This is just a method to set the textures right, so that you can map using gtkradiant and view your map in quake3 or elite force. DO NOT distribute your map for Quake 3 as the textures are copyright of Raven/LEC.
Copy the assets0.pk3 and the assets1.pk3 in your baseq3 directory.
Open the scripts subdirectory and edit the shaderlist.txt file. It should look like this :
Now open the assets0.pk3 file (with winzip) and extract the .shader files located in the /shader subfolder to your baseq3/scripts directory.
Now load gtkradiant and you should get all the textures, including the shaders
Mapper 4 Wired Lamp Studios