On a Linux server, you should have (in addition to Perl, but simpler) tools called grep and sed, which can find and find/replace strings in files. You can probably run these by cron if you can't do it any other way. The commands are complicated, but if it takes you 2 entire days of study to build the commands, and then 2 minutes to run them, it is still less work than spending several days cleaning files manually.
If you've downloaded files to your local PC and it's Linux, you can use grep, sed, or ssed, same as on the server.
If your PC is Windows, there are Windows versions of grep, and a version of sed called ssed (Super Sed).
Editors such as FrontPage, Dreamweaver, Expression Web also have powerful search/replace commands.