Website Chaos

Hey guys. So I'm volunteering this year for my university's College Dems group as the Media Chair. Which of course means I'm working primarily with our website. The only problem is the site suffered attacks a few months ago that no one knows how to fix, and is currently marked by Google as a website that may harm your computer.

Here's the diagnosis

Bottom line, I'm pretty good with computers, but issues like these are currently beyond my comprehension. I love learning more about how to deal with issues like these, but at the moment I don't know where to go to start fixing any of this. Any suggestions?

What kind of website is it? Does it use any 3rd-party software like content management systems or forum software? What language is the site written in? PHP? ASP.NET? Plain HTML?

I visited the site and it loaded fine for me without any warning.

To stop the warnings from happening, you need to sign up for Google Webmaster Tools which requires you to have FTP access to the site root.