Gotcha. File Integrity Monitoring (FIM) is a good one to have running. Albeit, I was saying in another post that most Magento compromises happen directly in the Database these days, as opposed to compromising file systems.
The Magento Security Tool scans for Malware if you’re not using it already. Plus it’s free. They’ve also been working on an SSH version which is supposed to be a little more powerful, but they’ve not released any details on the features yet. And for some reason, my SSL Certificate Provider does daily malware scans too.