Baffling theme issues

Apparently my site got hacked some time ago and I’ve done my best to clean it up but now my theme (a WPMU theme) is wonky and won’t render properly at all unless I’m logged in. (These issues may or may not have something to do with the extra security plugins I’ve added recently in order to defend against such attacks). I’ve also noticed (thanks to my Google Analytics Visits sidebar) that when not logged in the theme’s homepage has a discrepancy in the number of visits, indicating it has become static.

I’ve also noticed that when I’m logged in, on the index page the Links in the right sidebar are squished together but in every other Page they’re spaced like they should be, whereas on the left sidebar where I keep the Google Analytics Visits widget, all of the countries are spaced double than what they usually are.

My bloggers are also all getting 404 pages whenever they try to log in. These issues have all been befuddling me for a while now and I can’t seem to figure out what’s going on.

By the way, my site is on a private server using nginx.

Any suggestions or help would be greatly appreciated.