I don't know why your system is behaving as you describe. In relation to the second error message you describe:
stsmd-cgroups-agent failed to get D-Bus connection: failed to connect to socket /org/freedesktop/systemd1/private: connection refused.
I don't understand the failed connection to /org/... because there is no such directory on my system. What I do have is:
/usr/share/dbus-1/system-services/org.freedesktop.systemd1.service with the following contents:
# This file is part of systemd.
# systemd is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
I am wondering whether your dbus error has anything to do with this file. Perhaps you can check whether it exists, and if not, then copy this one in and reboot to see what happens. But before you do that, I also notice that in the directory /lib/systemd/system, there exist some dbus services: dbus.service, dbus.socket and the directory dbus.target.wants. Maybe if you enable all of these and start them with the systemctl command, it might make a difference. Enabling them them involves linking them into the /etc/systemd/system directory as root. Other than that, I'm pretty much out of ideas at the moment.