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Creating an ArcGIS for Server site can be done a few different ways; the brute force way is to uninstall and re-install the entire ArcGIS for Server application (and possibly a web adaptor if you're using one). However, the path you take will depend on your requirements and your specific situation. Besides ripping everything out and re-installing, here are two alternative methods for creating a site:
Deleting a Site and Creating a Brand New Site
This method assumes that you simply want to delete the current site and create a new one. In other words, you don't care about your current site and have no interest in saving any part of its configuration.
Step 1 - delete the existing site:
http://resources.arcgis.com/en/help/main/10.2/index.html#/Deleting_a_site/0154000005zw000000/
Step 2 - create a brand new site:
http://resources.arcgis.com/en/help/main/10.2/index.html#//0154000002p4000000
Backing Up a Site Configuration and Restoring It Afterwards
This method assumes that you are either moving your site to another machine (and have no interest in joining that other machine to your current site first) or that you are reverting your current site back to a previous state when you last backed it up.
Step 1 - back up the existing site:
http://resources.arcgis.com/en/help/main/10.2/index.html#/Backup_utility/01540000065s000000/
Step 2 OPTIONAL - delete the existing site:
http://resources.arcgis.com/en/help/main/10.2/index.html#/Deleting_a_site/0154000005zw000000/
Step 3 - restore the site
http://resources.arcgis.com/en/help/main/10.2/index.html#/Restore_utility/01540000065r000000/