This doesn't look like a typical RetroPie installation - what version of RetroPie do you have installed ?
You may have ran out of disc space on the sdcard, you can check that by exiting EmulationStation and looking at the welcome message.
The N64 emulator is installed from within the RetroPie-Setup script, not with the procedure you described.
The Errors are logged to ... message is a generic runcommand information message and doesn't mean an error has occurred, but in the event of an error, this is where it would be logged.
RetroPie setup already sets up one of the N64 Emulators ( I think Mupen64 ), so you don't have to install anything, especially macOS binaries that don't run on a RetroPie. Make sure your ROM is valid and try removing any game resolutions you've set, it seems the problem is from your TV not accepting the resolution you set.
I received my 8bitdo Zero 2 days back, still no luck configuring together with other 8bitdo controllers. Maybe downgrading the other 8bitdo controllers and switching the hack mode to on could help to get them to work all at the same time..