So ever since Apache moved to modular in version 2 you need to change your tune ups and modification for Apache in MPM instead of directly in apache
So to do this , firstly recompile Apache 2.2.8 in WHM/cPanel with the MPM prefork option enabled ( which is on the last screene of easyapache3 )
And after thats done you need to add your options here , the best way to do it is to add the following lines to httpd.conf
# Server-pool management (MPM specific)
# Various default settings
Then add the changes you want :
set your timeout
settings etc in
# Timeout: The number of seconds before receives and sends time out.
# KeepAlive: Whether or not to allow persistent connections (more than
# one request per connection). Set to "Off" to deactivate.
Then run the distiller to force cPanel to retain the changes