You wouldn't want to change any of the module files because they don't have php extensions. Instead you'd change the files that actually run Drupal, like index.php and update.php. I believe those are the only two files that are called directly by the browser. Everything else gets loaded by include(), so they should be run by PHP5 as well.

To avoid any unexpected "File not found" errors, I'd see if you can get godaddy to go in the other direction, and make PHP 4 have the special extension. I think they can do that on a directory by directory basis, so that shouldn't affect anyone else hosted on your server.
It seems Shawn beat me to it.