After setting the config file manually, the first time I run Moodle, it returns an error complaining that "mysqli is not supported by XMLDDB". This is caused by the fact that there is no mysqli directory within the lib/xmldb/classes/generators directory. After having a look at the mysql directory I saw no reason why I couldn't use the mysql.class.php file - so I created a new mysqli directory and copied mysql.class.php into mysqli as mysqli.class.php/ I then changed all references to mysql within the php file to mysqli.
After that Moodle had no problems, so it appears to be resolved. I am primarily posting the issue as I could find no reference to this problem, so I was unsure if you are aware of it.