Virus attack! – please advise

I started this thread cause I thought I just had rss problems but it turns out it was a virus.

My website is at veryserious.org, if you go there now you will just see an index.html I put there. But, if you’re not running IE, go to veryserious.org/index.php and then view the source. There is a bit of code that starts out “Yahoo! counter”.

This malicious little piece of js is all over my site and I has appended itself to every file that it can. It was on the wordpress dashboard pages even, until i reinstalled.

I don’t have shell access so I downloaded everything to my local machine and did a text search using agent ransack for any text matching “Yahoo! Counter”. I mostly just found html files that had been infected.

Strangely enough, the wordpress/index.php is uninfected:

https://veryserious.org/wordpress/index.php

My question is, which files go into making the index.php file?

https://veryserious.org/index.php

I need to know so I can clean them.