i dont know how to help w/ your main issue, but to get ur own config to stay, simply save ur httpd.conf in the /Database folder then in Startup/cron on the setup page simply type [scripting editor/post boot script/post boot]
mount –bind /Database/httpd.conf [where ever the original file is located]
that should survive any restarts and save u having to relink ur httpd.conf, i use it for my own blacklist.html
hope it helps
JC