Sorry not to get back to you sooner, I highly suspect the problem came from the shared server on Hostmonster, as I found out from Google they had over 7000 infected sites, yet they told me to my face it was security vulnerabilities on my website. (It just had the original files with original default theme in the previous OS Class version)
My long term solution is to move my account off their server and change to a better webhost.
The problem was they modified js files to spread the Trojans.
I would love to have that plugin you referred to, I know do regular full backups. It was odd because the website was barely 2 weeks online and I lost all new members and posts because I did not have enough experience to separate the bad files from the good ones. So I ended up doing a clean new install.
Thanks for your concern on this, please let me know where I can get that plugin that let's you know if files were changed.