This plugin found all the malicious scripts on my WordPress website and deleted all of it successfully except the bad code in my theme .php files.
The plugin and my theme didn't play nicely at first, so I e-mailed Eli (the developer). I told him what the problem was and he asked for the login credentials to my wordpress site and I faithfully provided them to him.
Within a matter of hours Eli had gone in and removed all the remaining bad scripts and had updated hid plugin.
Within the last week I've told several friends about this plugin.
Eli is constantly improving the plugin and is a genuine and great person.
This plugin will save you insane amounts of headache and time. If you have any problems with the plugin, simply e-mail Eli and he will be willing to help you personally.