One thing you might try is checking to see if there are any specific queries that are the culprit or if it's just the overall workload. You can turn on slow query logging and check that file from time to time. You'd need to edit the mysql config file and restart mysql. You'd add something like:
log-slow-queries=filename
long_query_time = 6
filename would be the path to where you want it to log. 6 can be changed to another number, this will make it log anything that takes longer than the specified number.
