Diagnosing ConnectionProblems

Application thread (Java server code) making database queries is
blocked on the query execution to return and the db connection does
not timeout. It happens during load test after about three days of
constantly making same type of application requests.

One article that I came across about diagnosing connection problems is
[dev.mysql.com]. Based on this I am setting log_warnings=2 in my
current test. But I am not sure if this is going to help because it
appears that only aborted connections will be logged. So I am looking
for suggestions on how to go about diagnosing this problem.

Other commands that I am using to determine the server status is: get
innodb status and get process list

My Environment:
MySQL Server: 5.0.22 - CentOS
Connector/J version: mysql-connector-java-3.1.13
JDBC connection parameters:
autoReconnect=false
connectTimeout=5000
socketTimeout=8000
wait_timeout on the server side is default (8 hours)

Thanks in advance.

- M