Any idea on how we were compromised? Is there a SMF exploit we need to look into?
Tricky one really. In the past when the site shared the same password with the database, I assume they exploited a vulnerability to obtain it, and then created FTP user accounts and had a field day. But now that is not the case and just last week we upgraded to MySQL 5.5, I have no idea how they got to upload some crap, even bypassing the SMF firewall while they did?
You could have always done it? If it's more pay your after then consider your salary doubled as of today.