Suddenly WordPress looking for something and centering everything

I hope someone here can figure this puzzle out. Suddenly WordPress is displaying “this page does not exist” (twice!) before it loads the rest of the page and everything in my template became centered. I had my ftp client open and perhaps I either dragged some files around, or deleted/overwritten something in root by mistake, I don’t know. I thought reinstalling WordPress from backend would do it, it didn’t. Then I thought reinstalling my theme would fix it, it didn’t do it either. In fact, the problem persists with any theme. Here is what it looks like.

I also have separate WP installation in a subdirectory here and a similar problem appeared at the same time (except for the centering). This leads me to believe that perhaps I had dragged some file from one directory to another. Do you know what file could be responsible for something like this? On the other hand, this could be a totally different problem. Please help and thank you in advance.