unable to run postgres with pg_ctl
When used to start the instance, pg_ctl accepts options to the postgres executable, passed with -o

From its manpage:


  -o options
       Specifies options to be passed directly to the postgres command.

       The options should usually be surrounded by single or double quotes
       to ensure that they are passed through as a group.



So your last command in the question should be amended as:

/usr/lib/postgresql/9.3/bin/pg_ctl start \
   "-D" "/var/lib/postgresql/9.3/main" \
   "-o -c config_file=/etc/postgresql/9.3/main/postgresql.conf"