Ok. From personal exsperiance that addon.ini file needs to be in you eqemu folder. That would take care of that first error.
[Quest] Warning - plugin.pl: Perl runtime error: open 'plugin.pl' No such file or directory at <eval 3> line 1.
This error I do belive is from no having the plugin.pl file in your eqemu folder as well.
http://www.eqemulator.net/forums/showthread.php?t=16120 is a really great walkthrough that has helped me get very close to having my server up and running. It also has the download for the plugin.pl file. As far as the command.pl file; I'm stuck there myself. The post before this one I started is in regards to this issue.
Hope I could be of any help, but remember I'm just a newb myself but one who has solved simular issues. Figure I would post my exsperiances.
Good luck,
J.