Only thing i saw here are general answers. /run/user/1000 resp. $XDG_RUNTIME_DIR is a tmpfs (somt. like a ramdisk) created by PAM (pluggable authentication module) on login, 1000 being your user id. It is more restricted in security and size than cache and should be used for small files where quick access or security matters. A common example are sockets.
You can delete it, it will just be regenerated next log in, but your very session will run into trouble, you should log out after (if you don’t just get booted out, that is).
And yeah, like others said; this is not Windows, you don’t have to, and shouldn’t, clean up anything outside your home dir.