Restarted that service and still the same.

It baffles me because it worked yesterday and I don't know what i have changed that has stopped it from working.

I upgraded PHP and it still worked.

I upgraded mysql this morning and I'm fairly sure it worked immediately after doing that.

Its not system-mysql, its just the mysqld service you want (the former is for the webconfig)

service mysqld restart

This works on port 3306...and you'll need to create a root password using the webconfig if you haven't already.

Yes I'm sure I did, I've done it again and restarted system-mysql & htpd services
But I'm still getting the same errors.
Maybe I need to reinstall ClearOS, I only installed it yesterday and I've broke it already!

Just noticed your last line, I have tried setting the existing website to both "mysqli" and "mysql" and nothing.
With the new site I don't get far enough to choose as the Joomla setup checks detect no database (which is a lie!)

Have you installed the php-mysql extension?

yum install php-mysql

If it still doesn't work - you may have more luck using the 'mysql' database type (note not the same as 'mysqli')