I was actually hoping to see a list of exactly what lines you typed into your SSH session to see what you could have done wrong in following the instructions. Small syntax errors etc.
Even better, a log file of your entire session. Was there any feedback to see if you could enter the cloned directory? Did changing permissions work successfully? And I guess at the end of the day, what else have you installed on your system? Especially mods. I’m assuming you are using Terminal on a Mac, from what I’ve seen you post before.
Did you modify the configuration file using something like nano? If not, and you just did a drag and drop with FileZilla, you might need go Chmod 755 the config file. I think it’s 755 from memory. I don’t use FileZilla myself, so have no idea what it does and doesn’t do/respect. I personally use either Transmit or Cyberduck as my go to for SSH/FTP etc for the last 20 years haha! (I’m stubborn and old)
My guess is that it is something went wrong following the instructions on the Github page.
But if you’re 100% sure you’ve followed the instructions, then I guess the only thing I can suggest for now is finding a spare SD micro card. Flashing a fresh OS, and see what happens if you follow follow the instructions again and install mupen from scratch.
It is strange that it worked for some people first try, yet didn’t for others, despite having the same hardware, same base environment and following the same instructions. As a side, seemingly the people who have it working know their way around a command line fairly well.
Did you also try using the FBTurbo graphics driver, as suggested earlier?
As a side, I don’t have the doom ROM but I tried Duke Nukem 64. Worked super smooth and fine, albeit horrible controls. You’ll need to edit your configuration if you want something useable. Eg, X is forwards, Y is backwards, dpad left right = rotate, and up/down is inverted. It’s shocking.
I couldn’t get Quake 1 or 2 working on Mupen. I haven’t tried fiddling, but since Doom is ID software too, chances are it may not work without some fiddling of your own. Basically what I’m saying is, if Doom 64 is your primary reason for having an N64 emulator, you may be in for a bit more of a bumpy ride configuring it yourself.