I attempted your method and the result was a .WAD file with:
- a new texturex smaller in size, hopefully less all unused textures
- a new pnames
- flats (hopefully only called for)
There were no textures in the resulting file.
If there's a chance you'd like to process this one through as a test, feel free. You can download the .WAD here: http://www.db4d.org/wads/jacobs_ladder_beta08.zip
I also noticed issues with animations in game. It appears that only the first texture within an animated sequence as described in animdefs is copied into the new texturex.
If you process this, please let me know how it turns out and what I need to do to end up with an output.wad that contains a texturex, pnames, and graphics files called for by the input.wad's maps, cutting all the fat.
I appreciate your help.