Fix my wordpress code. Can't load database, possibly a file missing. Expert needed.

Hi, I have managed to screw-up my wordpress site somehow. I am at the stage of giving up now. I need some help! The site owner is getting upset by the down time. Hopefully somebody can help. What happened?: The server got a virus off an old joomla version, and all sites were trying to inject a trojan. This stopped (when the host did something, probably cleaned it..) and i was then told to update versions of joomla and wordpress. I didn't. I have possibly deleted a file from the installation. I deleted 404 405 406 etc from some web folders. I remember thinking the 'silence is golden' php could be a virus, but looking and they all seem to be there. On sunday night site wasn't working and i think all the folders and wordpress softilisciuos i uninstalled i may have uninstalled the sql database. I restored the database but now all i get is the homepage css and i think most the [login to view URL] but no content. I get 404 which seems to be coming from the theme. I think it sees the database ok. I renamed it in wp-config. I need to get this working and sure someone can help. If you have a spare hour it would be great if you think you can fix it. Thanks