Will the access restrictions to root via changes to the /etc/pam.d/common-auth file mess up my settings (yubikey)
my common-auth file:
# Use this to use both your password + Yubikey. You can comment this line if you want to JUST use your Yubikey (NOT RECCOMENDED)
auth required pam_unix.so nullok_secure try_first_pass
# The line below is required to be able to use your Yubikey
auth [success=1 new_authtok_reqd=ok default=die ignore=ignore] pam_yubico.so mode=challenge-response
# Default rules
auth requisite pam_deny.so
auth required pam_permit.so
auth optional pam_ecryptfs.so unwrap
auth optional pam_cap.so