Optimize /Rewrite Mysql queries

Currently we are running (Rayzz)on an Adult YouTube Type site. The script load averages over 2-10 with only 1 instance of Apache and MySQL running, and with mysql enabled to log slow queries, we are seeing queries taking over 15 seconds, and up to 90 seconds and sometimes locks up. The SQL queries with Rayzz are EXTREMELY inefficient, we need the database to be "debugged" and re-written to make it more efficient,optimized and deal with the issue of closing every sql connection, after a script execution. Also need to make server secure against hackers and suggest tips to improve performance. Server is a dedicated linux server (Cpanel/WHM/ CentOs) running some MySQL & perl scripts. Check to see why the load is high and take steps to lower the load, securing and optimizing the performance of the servers & harden against attacks. Also need to make sure server hasn't already been comprimised. Need done ASAP, must have numerous references.