I'm using worldcraft to extract the original textures from the pak files but have had a problem extracting all textures from both pak files.
Worldcraft seems to be only extracting the textures from pak0 and not pak1, anyone know of a better way so I can make a texture wad of all original textures?

in Worldcraft there is a small utility called MakeTextures.. it does exactly what you ask +more (you can add to the wad file all textures in custom maps)

Cheers man, finally figured it out
Wasnt missing id textures it was the hipnotic textures from the expansion pack, I got a bit confused