Webdiggity wrote:So I should clamp down the user the web server runs under?
No, not specifically. It's just that I see some people (even on tutorials <gasp>) say that you should change the ownership of your web content to match the user that the web server runs under (usually the user is "apache", "httpd", or "nobody"). This is the exact wrong thing to do. The web user should not be able to write to any directory or file. There are very few limited exceptions to this (a counter data file for example needs to be written to by the web user). When someone exploits a vulnerability in your web server or in a PHP script they will be connected with the rights that the web server user has which means if that user owns all of your content then all of your content can potentially be changed by the cracker. That's why I asked you to list the permissions on the index.html files and the directories that they are contained in (ls -l index.html).
Also, since I already cleaned the files, is there a log that lists file modification history for my /home directory?
Got any incremental backups? :)
As I get the new server on line, would it be a good idea to have my logs periodically backup up and dumped to a safe place. I don't mind going overkill on the new rig.
Normally it's a good idea to have a remote syslog server so all of the system logs actually get written directly to another server entirely. That's really not feasible in your case.