Guide: rTorrent + ruTorrent installation

[Moodkiller]

Ok before I mess this up, thought I would ask. Currently I get these errors when I open ruTorrent

Spoiler (Click to View)

Code:

[09.11.2014 02:28:30] WebUI started.
[09.11.2014 02:28:33] rutracker_check: Plugin will not work. Webserver user must have execute access to the rtorrent session directory (/media/HDD1/Torrents/session/).
[09.11.2014 02:28:33] autotools: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] unpack: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] loginmgr: Some functionality will be unavailable. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] create: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] rutracker_check: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] history: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] rss: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] trafic: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] retrackers: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] ratio: Some functionality will be unavailable. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] scheduler: Plugin will not work. rTorrent user can't access external program (php).
[09.11.2014 02:28:33] screenshots: Plugin will not work. rTorrent user can't access external program (ffmpeg).
[09.11.2014 02:28:33] mediainfo: Plugin will not work. rTorrent user can't access external program (mediainfo).
[09.11.2014 02:28:35] DataDir plugin: rTorrent user can't access php interpreter. Plugin will not work.
[09.11.2014 02:28:35] Unpack plugin: rTorrent user can't access 'unrar' program.

As the error suggests, there is a permission issue. These are the settings I used when I ran the script:
Note the change of user to pi and the watch and download locations. Subsequently the relative mkdir sections were commented out of the script but I left the permission changes in. (see after the below code)

Spoiler (Click to View)

Code:

SCRIPT_NAME='rtorrent_pi.sh'
AUTHOR='koper89'
LOGFILE="/tmp/rtorrent_install.log"
USER='pi'

# WWW SETTINGS
WWW_DIRECTORY='/var/www'         # Do not include a slash at the end of the path

# RTORRENT SETTINGS
RTORRENT_USER='pi'            # Permissions
RTORRENT_GROUP='pi'           # Permissions
MAX_PEERS_SEED='50'
MIN_PEERS_SEED='2'
MAX_PEERS='50'
MIN_PEERS='2'
PORT_RANGE='61040-61050'
MAX_UPLOADS='30'
DOWNLOAD_RATE='0'
UPLOAD_RATE='0'
MAX_DOWNLOADS_DIV='0'
MAX_UPLOADS_GLOBAL='70'
MAX_DOWNLOADS_GLOBAL='50'
DHT='disable'
DHT_PORT='6881'
PEER_EXCHANGE='no'
SESSION_DIRECTORY='/media/HDD1/Torrents/session'
WATCH_DIRECTORY='/media/HDD1/Torrents/Torrents'
DOWNLOAD_DIRECTORY='/media/HDD1/Torrents'
RTORRENT_CONFIG='/home/pi'
RTORRENT_SOCKET='/tmp/rtorrent.sock'
NICE='7'                        #Nicelevel of rtorrent

# RUTORRENT SETTINGS
PORT='9096'                     #port for rutorrent website http://localhost:PORT
PLUGINS='y'                     #install plugin pack with f.e. unpack (unrar)
PLUGINS_URL='http://dl.bintray.com/novik65/generic/plugins-3.6.tar.gz'
RUTORRENT_URL='http://dl.bintray.com/novik65/generic/rutorrent-3.6.tar.gz'

Folder creations commented out:

Spoiler (Click to View)

Code:

echo 'Creating rTorrent watch directory...'
#sudo mkdir -p "$WATCH_DIRECTORY" >>"$LOGFILE" 2>&1
sudo chown $RTORRENT_USER:$RTORRENT_GROUP "$WATCH_DIRECTORY" >>"$LOGFILE" 2>&1
#sudo chmod 777 "$SESSION_DIRECTORY" >>"$LOGFILE" 2>&1

echo 'Creating rTorrent session directory...'
sudo mkdir -p "$SESSION_DIRECTORY" >>"$LOGFILE" 2>&1
sudo chown $RTORRENT_USER:$RTORRENT_GROUP "$SESSION_DIRECTORY" >>"$LOGFILE" 2>&1
#sudo chmod 777 "$SESSION_DIRECTORY" >>"$LOGFILE" 2>&1

echo 'Creating rTorrent download directory...'
#sudo mkdir -p "$DOWNLOAD_DIRECTORY" >>"$LOGFILE" 2>&1
sudo chown $RTORRENT_USER:$RTORRENT_GROUP "$DOWNLOAD_DIRECTORY" >>"$LOGFILE" 2>&1
#sudo chmod 777 "$DOWNLOAD_DIRECTORY" >>"$LOGFILE" 2>&1

Edit: This also shows up when I open ruTorrent:


As the main OP stated to log in as root, the very first command I did was sudo su followed by wget onwards. Did this have anything to do with the permissions not being granted to those that need it? And the end question being, could someone help me fix this please?