timeout error

Any idea why my server continues to time out on my upgrade? I made the recommended changes in php.ini

max_execution_time = 14400
max_input_time = 14400
session.gc_maxlifetime = 14400
memory_limit = 2048M

I also edited the code in the 

moodle/lib/file_storage/file_storage.php

moodle/lib/moodlelib.php

to reflect the longer 14400 length of time. Anywhere else I should be trying to avoid the timeout from occuring? Thanks

I also read on here that it could be recommended to change 

mysql wait_timeout settings to 400

I couldn't find that php setting in mine although I did find a 

mysql.connect_timeout Might that be the same? I am running php 5.3.5

Thanks again for any ideas here