BEFORE YOU READ ANY MORE OF THIS POST BACKUP YOUR DB AND FILES!
First of all read the first line again, don't skip it.
I think that you have done one of two things wrong:
your permalink s include the site url somehow or your site url is set wrong.
Look CAREFULLY at a link that I grabbed from your site:
notice that the second http is written http:/ with just one slash. you need to get that fixed first.
Reset your permalinks to the default, then go to settings general and be sure that the site url and home are set correctly.
If this does not work, delete your .htaccess file from your site (just remane it to htaccess.txt and then reset your permalinks again, this will allow WordPress to re-create it.
If that does not work, check out this script: http://interconnectit.com/124/search-and-replace-for-wordpress-databases/
search for http:/www.rooftoprunners.com and replace with http://www.rooftoprunners.com