clean malware from site and fix address issue. Oscommerce

I have a site which is no longer redirecting to the correct place so it will not load it is a oscommerce site it is showing ..../catalog but should be catalog/[login to view URL] to work so that needs fixing also it has a bit of malware, i was told by my host to clean the htaaccess file google shows it as being an infected site so it must be cleaned throughout its not a huge site so its not a huge job i also need the oscommerce updated to the latest version but it is a customised site with sts templates installed so its not straightforward only respond i u have the required expertise