Firstly – when installing the server, do not select to create the symbolic link – softlink if you are installing into the default locations.
Also I had the usual problem where xwindows could not display the setup program. The error was
“Please edit your shell's DISPLAY environment variable to
reflect an unlocked terminal that you would like to launch
the Domino Setup Program”
The fix was to su to root and run the command /usr/X11R6/bin/xhost
then as the “notes” user run...
Once this is done cd to the /local/notesdata directory and run /opt/ibm/lotus/bin/server to start the setup program.