Hello Jorge,
That's a wrong way to access or test and chech if the handle server is running and the error you saw is expected just ignore it.
1) To help you make systemd take care of running the handle server at boot time you need to copy and paste what you see in red below into the terminal and just do the other steps to activate it.
sudo cat << EOF > /usr/lib/systemd/system/handle-server.service
[Unit]
Description=Handle Service
After=network.target tomcat9.service
[Service]
Type=oneshot
RemainAfterExit=yes
ExecStart=/opt/dspace/bin/start-handle-server
ExecStop=/bin/kill $MAINPID
User=tomcat
Group=tomcat
[Install]
WantedBy=multi-user.target
EOF
2) systemctl daemon-reload
3) systemctl enable handle-server.service
4) systemctl start handle-server.service
5) systemctl status handle-server.service
Regarding the other issues you mentioned I hope someone else step in and help you with them because it needs more details and debugging to approach it. Tim? :-).
BR,
Mo.