I accidentally deleted some important lines because I tried to just change the time out command but didn't realize I had to change them all at once.
Al my sites were down that hole time, and I almost had a brain spasm. But thanks for the info. Although I havent tested it yet Im sure it works.

skip-locking
character-sets-dir=/usr/share/mysql/charsets/
query_cache_limit=1M
query_cache_size=16M
query_cache_type=1
max_user_connections=100
max_connections=250
interactive_timeout=120
wait_timeout=1800
connect_timeout=3000
thread_cache_size=96
key_buffer=16M
join_buffer=2M
max_allowed_packet=16M
table_cache=1024
record_buffer=2M
sort_buffer_size=1024K
read_buffer_size=1024K