So, the icons work now, but look like this?http://img697.imageshack.us/img697/566/unrecognizedfiletypeicog.png
I'm not sure if there's a way to easily change them all. You can change them one by one in the file properties.
I would suggest using ccleaner to scan/clean your registry. Often after that many infections, there is some clutter in the registry that needs tidying up.http://www.piriform.com/ccleaner