Edit the wads with SLADE3 and replace the MIDIs with the ones in their assigned MIDI packs (which you also open using SLADE3). Then run wadsmoosh and it should work.
I couldn't get this to work since MASTER (The Master Levels) and NERVE (No Rest for the Living) use the Doom II MUS files.
Any chance WadSmoosh will ever support mapping either of those Episodes to different sets of music so we can replace them with Music Packs?
For example, I was able to replace the Plutonia music by renaming all the D_ files to P_. It would be great if all MASTER & NERVE MUS files were prefixed with M_ & N_ respectively. This would allow us to use their respective community music packs.