are you setting up the live server or a development server
the config can be easily enough changed after you've got it working for the first time
confiiguring a server is not fo rthe faint hearted, it depends on a lot of knowledge, the available hardware and so on.
if you need 1000+ concurrent connections then you should be able to afford to bring in expert help. for now just get the dam thing awake and complete your development work. again Id strongly reccommend you use a clean install and if possible consider using an XAMPP package, although Ive never had a problem with a MySQL binary install either