Upgrade to Ubuntu Server 16.04.1 LTS appeared fine, Python and other issues arise

Question

I'm kind of at shooting an arrow into the darkness right now because I'm not sure really what happened to my server. It went through a distribution upgrade a little while back and everything seemed fine, but now after some reboot it appears that my python installation got screwed up and I'm not sure how to recover. This has caused problems with update/upgrade as well as running software like transmission (I'm assuming this is related anyways. I'm just going to post whatever I can here and hopefully it'll be enough to get some help from you all. Thanks again in advance!

wyth@server:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.1 LTS
Release:        16.04
Codename:       xenial


wyth@server:~$ sudo apt-get update
Hit:1 http://us.archive.ubuntu.com/ubuntu xenial InRelease
Get:2 http://us.archive.ubuntu.com/ubuntu xenial-updates InRelease [95.7 kB]
Hit:3 http://us.archive.ubuntu.com/ubuntu xenial-backports InRelease
Get:4 http://security.ubuntu.com/ubuntu xenial-security InRelease [94.5 kB]
Fetched 190 kB in 0s (218 kB/s)
keys on reference is experimental at /usr/bin/apt-show-versions line 264.
keys on reference is experimental at /usr/bin/apt-show-versions line 359.
Reading package lists... Done

wyth@server:~$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
 gstreamer1.0-clutter : Depends: libcogl15 (>= 1.15.8) but it is not installable
 libcwidget3 : Depends: libsigc++-2.0-0c2a (>= 2.0.2) but it is not installable
 libmutter0c : Depends: libcogl15 (>= 1.15.8) but it is not installable
 libnux-4.0-0 : Depends: libsigc++-2.0-0c2a (>= 2.0.2) but it is not installable
 python : Depends: python-minimal (= 2.7.5-5ubuntu3) but 2.7.11-1 is installed
 python-all : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-all-dbg : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
                  Depends: libpython-all-dbg (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-all-dev : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
                  Depends: libpython-all-dev (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-dbg : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
              Depends: libpython-dbg (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-dev : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
              Depends: libpython-dev (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 synaptic : Depends: libxapian22 but it is not installable
 zeitgeist-core : Depends: libxapian22 but it is not installable
E: Unmet dependencies. Try using -f.

wyth@server:~$ sudo apt-get -f install
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
  appmenu-qt distro-info-data gir1.2-gconf-2.0 gir1.2-gnomebluetooth-1.0 gnome-accessibility-themes
  gnome-themes-standard indicator-appmenu libdbusmenu-qt2 libept1.4.12 libgdata13 libgphoto2-l10n libgupnp-av-1.0-2
  libjasper1 libjson0 libmediaart-1.0-0 libnl-route-3-200 libtracker-sparql-0.16-0 libupower-glib1 libxcb-util0
  linux-image-3.13.0-85-generic linux-image-extra-3.13.0-85-generic mutter-common python-gconf telepathy-indicator
  watershed
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  gstreamer1.0-clutter libencode-locale-perl libept1.5.0 libfile-desktopentry-perl libfile-listing-perl
  libfile-mimeinfo-perl libfont-afm-perl libglewmx1.13 libhtml-form-perl libhtml-format-perl libhtml-parser-perl
  libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl
  libhttp-message-perl libhttp-negotiate-perl libio-html-perl liblwp-mediatypes-perl liblwp-protocol-https-perl
  libnet-dbus-perl libnet-http-perl libnux-4.0-0 libnux-4.0-common libpython-all-dbg libpython-all-dev libpython-dbg
  libpython-dev libpython-stdlib libtie-ixhash-perl libvte-2.91-0 libvte-2.91-common libwww-perl
  libwww-robotrules-perl libx11-protocol-perl libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl python
  synaptic xdg-utils zeitgeist-core
Suggested packages:
  libdata-dump-perl libcrypt-ssleay-perl libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl
  xml-twig-tools python-doc python-tk dwww menu deborphan gvfs-bin
The following packages will be REMOVED:
  libcwidget3 libmutter0c
The following NEW packages will be installed:
  libencode-locale-perl libept1.5.0 libfile-desktopentry-perl libfile-listing-perl libfile-mimeinfo-perl
  libfont-afm-perl libglewmx1.13 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tree-perl libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl
  libhttp-negotiate-perl libio-html-perl liblwp-mediatypes-perl liblwp-protocol-https-perl libnet-dbus-perl
  libnet-http-perl libtie-ixhash-perl libvte-2.91-0 libvte-2.91-common libwww-perl libwww-robotrules-perl
  libx11-protocol-perl libxml-parser-perl libxml-twig-perl libxml-xpathengine-perl xdg-utils
The following packages will be upgraded:
  gstreamer1.0-clutter libnux-4.0-0 libnux-4.0-common libpython-all-dbg libpython-all-dev libpython-dbg
  libpython-dev libpython-stdlib python synaptic zeitgeist-core
11 upgraded, 32 newly installed, 2 to remove and 866 not upgraded.
6 not fully installed or removed.
Need to get 0 B/4,425 kB of archives.
After this operation, 4,390 kB of additional disk space will be used.
Do you want to continue? [Y/n] y
Extracting templates from packages: 100%
Setting up python-minimal (2.7.11-1) ...
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/local/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/usr/local/lib/python2.7/compileall.py", line 16, in <module>
    import struct
  File "/usr/local/lib/python2.7/struct.py", line 1, in <module>
    from _struct import *
ImportError: No module named _struct
dpkg: error processing package python-minimal (--configure):
 subprocess installed post-installation script returned error exit status 1
Errors were encountered while processing:
 python-minimal
E: Sub-process /usr/bin/dpkg returned an error code (1)

wyth@server:~$ sudo apt-get install --reinstall python2.7
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these:
The following packages have unmet dependencies:
 gstreamer1.0-clutter : Depends: libcogl15 (>= 1.15.8) but it is not installable
 libcwidget3 : Depends: libsigc++-2.0-0c2a (>= 2.0.2) but it is not installable
 libmutter0c : Depends: libcogl15 (>= 1.15.8) but it is not installable
 libnux-4.0-0 : Depends: libsigc++-2.0-0c2a (>= 2.0.2) but it is not installable
 python : Depends: python-minimal (= 2.7.5-5ubuntu3) but 2.7.11-1 is to be installed
 python-all : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
 python-all-dbg : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
                  Depends: libpython-all-dbg (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
 python-all-dev : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
                  Depends: libpython-all-dev (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
 python-dbg : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
              Depends: libpython-dbg (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
 python-dev : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
              Depends: libpython-dev (= 2.7.11-1) but 2.7.5-5ubuntu3 is to be installed
 synaptic : Depends: libxapian22 but it is not installable
 zeitgeist-core : Depends: libxapian22 but it is not installable
E: Unmet dependencies. Try 'apt-get -f install' with no packages (or specify a solution).

I'm happy to post whatever other pertinent info you guys would find helpful. Also, here are the errors I get when trying to start transmission:

wyth@server:~$ sudo service transmission-daemon start
Job for transmission-daemon.service failed because a fatal signal was delivered to the control process. See "systemctl status transmission-daemon.service" and "journalctl -xe" for details.

wyth@server:~$ systemctl status transmission-daemon.service
● transmission-daemon.service - Transmission BitTorrent Daemon
   Loaded: loaded (/lib/systemd/system/transmission-daemon.service; enabled; vendor preset: enabled)
   Active: failed (Result: signal) since Sat 2016-11-19 22:42:54 EST; 37s ago
  Process: 4453 ExecStart=/usr/bin/transmission-daemon -f --log-error (code=killed, signal=SEGV)
 Main PID: 4453 (code=killed, signal=SEGV)

Nov 19 22:42:54 server systemd[1]: Starting Transmission BitTorrent Daemon...
Nov 19 22:42:54 server systemd[1]: transmission-daemon.service: Main process exited, code=killed, status=11/SEGV
Nov 19 22:42:54 server systemd[1]: Failed to start Transmission BitTorrent Daemon.
Nov 19 22:42:54 server systemd[1]: transmission-daemon.service: Unit entered failed state.
Nov 19 22:42:54 server systemd[1]: transmission-daemon.service: Failed with result 'signal'.

Edit: Another symptom is that it appears disconnected as the network drive. However, I can still ssh into it and see my files and etc.

Update: This is the contents of /etc/apt/sources.list

# deb cdrom:[Ubuntu-Server 12.04.2 LTS _Precise Pangolin_ - Release i386 (20130214)]/ precise main restricted

# deb cdrom:[Ubuntu-Server 12.04.2 LTS _Precise Pangolin_ - Release i386 (20130214)]/ precise main restricted

# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://us.archive.ubuntu.com/ubuntu/ xenial main restricted
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial main restricted

## Major bug fix updates produced after the final release of the
## distribution.
deb http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-updates main restricted

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ xenial universe
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial universe
deb http://us.archive.ubuntu.com/ubuntu/ xenial-updates universe
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://us.archive.ubuntu.com/ubuntu/ xenial multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial multiverse
deb http://us.archive.ubuntu.com/ubuntu/ xenial-updates multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-updates multiverse

## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse

deb http://security.ubuntu.com/ubuntu xenial-security main restricted
deb-src http://security.ubuntu.com/ubuntu xenial-security main restricted
deb http://security.ubuntu.com/ubuntu xenial-security universe
deb-src http://security.ubuntu.com/ubuntu xenial-security universe
deb http://security.ubuntu.com/ubuntu xenial-security multiverse
deb-src http://security.ubuntu.com/ubuntu xenial-security multiverse

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu precise partner
# deb-src http://archive.canonical.com/ubuntu precise partner

## Uncomment the following two lines to add software from Ubuntu's
## 'extras' repository.

And these are the files in /etc/apt/sources.list.d/

wyth@server:/etc/apt/sources.list.d$ ls -lha
total 32K
drwxr-xr-x 2 root root 4.0K Nov 20 09:02 .
drwxr-xr-x 6 root root 4.0K Sep  8  2014 ..
-rw-r--r-- 1 root root  176 Nov 11 23:32 mc3man-trusty-media-trusty.list
-rw-r--r-- 1 root root  176 Nov 11 23:32 mc3man-trusty-media-trusty.list.distUpgrade
-rw-r--r-- 1 root root   54 Nov 11 23:32 plexmediaserver.list
-rw-r--r-- 1 root root   54 Nov 11 23:32 plexmediaserver.list.distUpgrade
-rw-r--r-- 1 root root  104 Jan 23  2016 plexmediaserver.list.dpkg-old
-rw-r--r-- 1 root root  104 Jan 23  2016 plexmediaserver.list.save

Update: Deleted the unnecessary files from /etc/apt/sources.list.d as per @ThatGuy's instructions. apt-get update works, but apt-get upgrade is still broken. Transmission still refuses to start.

wyth@server:/etc/apt/sources.list.d$ ls -lha
total 16K
drwxr-xr-x 2 root root 4.0K Nov 20 20:03 .
drwxr-xr-x 6 root root 4.0K Sep  8  2014 ..
-rw-r--r-- 1 root root  176 Nov 11 23:32 mc3man-trusty-media-trusty.list
-rw-r--r-- 1 root root   54 Nov 11 23:32 plexmediaserver.list

wyth@server:/etc/apt/sources.list.d$ sudo apt-get update
Hit:1 http://us.archive.ubuntu.com/ubuntu xenial InRelease
Get:2 http://us.archive.ubuntu.com/ubuntu xenial-updates InRelease [95.7 kB]
Hit:3 http://us.archive.ubuntu.com/ubuntu xenial-backports InRelease
Get:4 http://security.ubuntu.com/ubuntu xenial-security InRelease [94.5 kB]
Get:5 http://us.archive.ubuntu.com/ubuntu xenial-updates/main i386 Packages [418 kB]
Fetched 608 kB in 1s (581 kB/s)
keys on reference is experimental at /usr/bin/apt-show-versions line 264.
keys on reference is experimental at /usr/bin/apt-show-versions line 359.
Reading package lists... Done

wyth@server:/etc/apt/sources.list.d$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
 gstreamer1.0-clutter : Depends: libcogl15 (>= 1.15.8) but it is not installable
 libcwidget3 : Depends: libsigc++-2.0-0c2a (>= 2.0.2) but it is not installable
 libmutter0c : Depends: libcogl15 (>= 1.15.8) but it is not installable
 libnux-4.0-0 : Depends: libsigc++-2.0-0c2a (>= 2.0.2) but it is not installable
 python : Depends: python-minimal (= 2.7.5-5ubuntu3) but 2.7.11-1 is installed
 python-all : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-all-dbg : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
                  Depends: libpython-all-dbg (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-all-dev : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
                  Depends: libpython-all-dev (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-dbg : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
              Depends: libpython-dbg (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 python-dev : Depends: python (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
              Depends: libpython-dev (= 2.7.11-1) but 2.7.5-5ubuntu3 is installed
 synaptic : Depends: libxapian22 but it is not installable
 zeitgeist-core : Depends: libxapian22 but it is not installable
E: Unmet dependencies. Try using -f.

wyth@server:~$ sudo service transmission-daemon start
Job for transmission-daemon.service failed because a fatal signal was delivered to the control process. See "systemctl status transmission-daemon.service" and "journalctl -xe" for details.