Hi
Both version should be correctly stopped. pg_upgrade started clusters itself.
Please check pg_upgrade_server.log file in directory where pg_upgrade was run.
Also where is postgresql.conf? In PGDATA? Otherwise you need tell pg_upgrade correct path, for example with options '-o
"-c config_file=/etc/postgresql/8.4/main/postgresql.conf" -O " -c
config_file=/etc/postgresql/9.4/main/postgresql.conf"'
regards, Sergei