After spending an entire day yesterday cleaning up the folder for one out of 30 websites on the same server, this was a job of a bot. A Sr. Malware Researcher at Sucuri helped me decode all the encoded php files I was unable to decode myself, to determine that it is just a bot that sets up to spam email with your server. Since I use a VPS with debian, I installed maldetect to scan all my files and it had found one file I was missing that was added to use google libraries plugin folder.
Before using maldetect, I was using threat scanner wordpress plugin to find all instances of eval. There were a ton of files modified and added to random folders (galleries, upload folder, and other plugin folders).
Maldetect probably would of been enough to determine what needed to be quarantined (or in my case, just went ahead and deleted since I could tell what was bad and what wasn’t by doing comparing between original plugin packages). I have since tightened things up with iTheme security plugin, and of course maldetect on the server side.