Spending three hours a day on the South Shore Line would make anyone depressed!
I bet you can get a software internship gig near you. Contact professors doing computational work at Notre Dame (http://ibms.nd.edu/clusters/computational-biology-bioinforma...) they may have room in their budget. Though the pay will not be extravagant.
As pragmatic as your solution of deleting the article is, I don't think that should be the action Fisher has to take here, it simply doesn't seem fair. If an employer takes issue with an article like that, then that's your indicator that they aren't right for you to begin with. But I have no experience with any of this so I can't conclusively say much.
I'm deleting the article tonight but I wanted to make sure people got the whole story and I didn't mention the company at all.
I'll definitely look into getting an internship gig and probably spend all of tonight and tomorrow applying for the software gigs that I think I'll be a good fit in. Still debating suing.