If you're still having problems, I would recommend reading this thread:
http://eqemulator.org/forums/showthread.php?t=30773 and using the script described there.
I started out with trying to use the Debian guide, and had a lot of problems along the way. Snag the later version of the script from that other thread, and then add into the section where it adds links a link for commands.pl and login.ini. I'm not sure of the exact directory locations at this time. You might be able to get that setup script working with your existing installation, but you may need to rename some directories or move things around. I know that the script creates a lot of soft links into the server directory that you do not create (and need) when using the Debian guide.
If you're planning on running your own login server and running locally only in your LAN, I would recommend setting the address and local address values in eqemu_config.xml. A couple of guides out there say it is unnecessary, but I had to do that in order to get up and running.