Debian server administration, security, and optimization

I have a new Debian 5 server (LAMP), DNS served by easyDNS. I am hosting a number of Drupal websites on the server through the use of Aegir and am having trouble with the server randomly crashing. I believe one of the tables in mysql may be missing an index (mysqld is running high in CPU), I am just being pounded by bots, or both. I need someone to look through the potential mysql issue and also make some suggestions/adjustments for handling bots and lowering the CPU usage. I can pinpoint the problem to one particularly robust site. The issue started once it was added to the server. * You must be familiar with LAMP and server administration especially * This is an unmanaged server with no phpmyadmin installation or cpanel * Shell access and mysql command line access will be provided, that is all If you are not comfortable with fixing an issue having only the above information then you are not likely the candidate for the job, do not bid. Otherwise, bid and I am excited to find someone to help out.