Warning: too many errors from [mirror]

It doesn’t give a message like that. You know it tried other mirrors because it successfully downloaded the DBs and completed.

The pacnew files are created by pacman. See: https://wiki.archlinux.org/title/Pacman/Pacnew_and_Pacsave

The endeavouros-mirrorlist is the EOS-specific mirrors.

The hooks directory is a place to store pacman hooks.

The gnupg directory contains pacman’s keyring.