[libretro ERROR] retro_load_game: couldn't read WAD header from '/home/pi/RetroPie/roms/ports/doom/doom2/DOOM2.WAD' [INFO] [Environ]: SET_MESSAGE: ROM loading failed... [ERROR] Failed to load content

Looks like it doesn't like your WAD. Try using another source. I've found one that works; I can't tell you where to get it but I can probably get away with sharing the crc32 and md5sum to help you determine if you've found the right one:

pi@retropie:~/RetroPie/roms/ports/doom/doom2 $ crc32 DOOM2.WAD ec8725db pi@retropie:~/RetroPie/roms/ports/doom/doom2 $ md5sum DOOM2.WAD 25e1459ca71d321525f84628f45ca8cd DOOM2.WAD