To add to this, don't forget that % and _ are both special characters in SQL. It is, however, much safer (harder to make mistakes) to limit input to the characters you want (e.g. [a-zA-Z0-9]) than to hope that you have a complete list of all SQL special characters.
IPTables can limit the number of connections an IP address can make in a given time limit and will simply drop packets until the IP address is below the limit again. You can also limit IP addresses by bandwidth in a given time limit. I'm sure other firewalls will have similar capabilities. Filtering such as this should be done as early as possible in the path through your system as that is where it has already had the least impact on the other users of your system.
I don't have a problem with calling your super user "root" but there is no harm in changing it. You should, however, definitely not allow this user to log in over the network. If the root user can log in over the network then an attacker brute forcing his way in already knows one username (and it's the most powerful user to boot)
Strangely enough, this post is almost not about PHP at all, but security involves the entire system so we shouldn't just focus on PHP anyway.
Thanks for the tips.