Does your company's IT department support Macs? If so, I'm not sure I would trust them to clean out the "virus" if that's their first suggestion for a full hard drive. That's a sign that they don't know much about Macs. If they don't support Macs, I wouldn't advise you to let them anywhere near your machine.
You keep referring to duplicate files... what are they called, and where are they found? That information is vital if you want any assistance here.
As to the corporate firewall blocking access... blocking access to what? Find out what IP address is being blocked, if it's blocking access to a specific IP address. We really need a lot more information than you're giving us. I hate to leave you entirely in the hands of an IT department that is, from the sounds of it, unlikely to be able to solve your problem, but we won't have any choice without better information.