@mahcneto
I think for the music to work with the custom WAD fdoom, you'd need to also have a copy of the music in ~/RetroPie/roms/ports/doom/fdoom.
You should be able to make symbolic links to the MP3 (so you don't have to copy them to your custom WAD directory which will save space).

Try something like this:
ln -s ~/RetroPie/roms/ports/doom/*.mp3 ~/RetroPie/roms/ports/doom/fdoom/

Let me know if this works because I am theorizing :-)