Here's what I would do:
-Set the folder with all the files to read only for all users except yourself
-Upload the files to security response
-Upload a few to www.threatexpert.com to see if they are communicating anywhere outside the network as well as to see what system changes they are making
-Delete all of the suspect files from that folder
-Disable autorun
-Block any communication/changes the threats are making according to the threatexpert report
-Once you get a detection for the threats from security response scan all machines in the network to ensure they are clean
-Change the folder back from read only