Hi @Justin_Netmore
Please visit following url New JavaScript Malware Issue on magento security center.
You should follow the steps mentioned under To Remove Malicious Code: also follow the best practices mentioned on the following link Magento Security Best Practices.
I also suggest you to
1) Apply all the patches released by Magento.
2) Use IP address restriction for the your magento admin.
3) Remove all the usernames and passwords which you created for any of the third parties to work with you as soon as work is completed.
4) Change your FTP, cPanel and other passwords with more secure passwords.
5) Try to use SFTP instead of FTP as it is more secure.