Desktop items & start menu items missing/hidden after virus

Okay, so my computer got infected and I downloaded paid versions of SuperAntiSpyware & Avira Antivirus and ran them plus a bunch of others from the Malware thread and was able to clean up my system but a bunch of my shortcuts on my desktop disappeared and my Start Menu is messed up. I was able to manually put a few of my shortcuts back on to my desktop but they showed up dimmed like they were hidden. I went and double checked in Folder Options to show hidden files and that was already selected. I downloaded and ran UnHide and all it did was make the dimmed shortcuts turn back normal but did not put all the others back. Also, if I try to open c:/Documents and Settings it pops up that it is not accessible and access is denied. The folder is also dimmed like it is hidden.

So at this point I don't know what else to do. :confused

Running Vista 64-bit

TIA