I previously had a 10 step process to replace all the files in a wordpress, this got rid of most file based exploits.
Since then i have written a shell script that pretty much incorperates that
wget http://blog.rimuhosting.com/files/restorewordpress.sh chmod +x restorewordpress.sh ./restorewordpress.sh /full/path/to/documentroot
Note: This does not do custom themes or plugins (only ones from wordpress.com), and its a good idea to double check the wp-config.php is clean, either before, or immediately after doing this.
Please let me know if you have any issues at all with this script, or modifications needing to be made.