Cleaning of 2 Infected Websites (used as a DDOS, we think)

We have two backed up sub domains that we've since removed from our server. Both of these subdomains (that were resident on the same hacked domain) contain many DDOS injections in the Javascript pages (and probably others). We need someone experienced in security, linux, and preferrably Joomla to help us clean these two domains out completely. Thank you.