It sounds like you are doing the right things to fix the problem. It may take Google a couple weeks to recrawl your site and update the data in the webmaster tools.
Should be easy to setup the link generation basically if the index.php is present you replace it with an empty string. And then for the request if you see index.php in it you issue a 301 redirect to the home page.
Otherwise whatever code generates the links may keep injecting the index.php string with the urls and I have no idea how many problems you're going to face.