Regarding your suspicious files, which maybe infected as you think, you could on line check them at: https://www.virustotal.com/
, just need to upload the suspicious file and check. For to get the files to your desktop, install WinSCP (Freeware) and copy those files to your pc from where you could freely upload them without any interference on your running server.
If you don't have WinSCP, download from: http://winscp.net/eng/index.php
install on your desktop under Windows and use the SSH settings for to connect to your server. If you run Linux on your destop, use an SCP Client for linux instead.