osCommerce Javascript Trojan Virus Removal

There has been a javascript trojan injected into the website. My antivirus software is saying the site has JS/TrojanDownloader.Pegel.AA. The virus had infected all javascript files and files containing "index" in the filename. All noticeable modifications to the codes of these files has been removed but the trojan is still present. This virus injects a script into the code when loading the page, but I'm not sure where it's pulling the javascript from since I had already removed all instances of this code in the php and js files. It seems that the virus is now only affecting the main index page and admin (backend) index page. I need an expert with experience in removing these type of virus from osCommerce stores and prevent this virus in the future. Please only bid if you have experience in doing this type of work. Thank you.