Although I don't have the same problem, I have been having troubles having this working. Though I feel I am so close. I think it is hard to grasp the instructions, but it is not the Authors fault due to their locality. I think I have got most of it nailed, eg. wordpress in the root of Zencart e.t.c. Just me being dense and missing the finer points maybe. lol

As far as I understand, you don't need to remove the index.php from WP-Content.