Accidentally scanned OSX from Bootcamp and OSX reset

Oh god, I've screwed up my mac beyond repair and I failed to utilize time machine based on the price of the time capsule. I'm a college student and simply cannot afford a $250 piece of hardware that I may never use. But now I'm paying for my arrogance in assuming I'd never need it. Sometimes I really hate myself.
I have, somehow, reset my entire OSX. The Dock is now huge, all of my icons are now reset to the default ones when I originally bought the Macbook Pro. The software is still there but the icons have been reset. The icon no longer bounces when I open it.
And I know exactly why. I was in Windows through bootcamp doing routine maintenance and decided to do a full scan using Microsoft Security Essentials. I forgot to have it ignore the E:/ drive which is where MacOSX installed. It must have got 25% through scanning it before I realized it. I don't even know if that can cause a problem but it obviously did. I booted into OSX just to double check everything was ok. It loaded fine, all icons where there and seemed like everything was ok. Except the icons weren't bouncing when I opened up an application even though it was checked in the preferences. This frustrated me so I rebooted again to see if that would fix the issue and now here I am. Completely back to factory defaults. My software is still there but the Dock reset itself and it seems as if other things reset. I'm doomed. So how do I start a reinstall process? Insert the Snow Leapord disk?
I'm worried because I have Parrallels 6 and if I have to reinitiate a bootcamp then I'm going to have to go buy another full non-upgrade version of Windows 7. Christ, my life really is terrible at the moment. Somebody please tell me I'm overreacting and focusing on the worst possible scenario.

Ok I think I lucked out. I trashed the dock.plist file and then ran Onyx and had it do EVERYTHING. I think it worked. The dock reset so I'll have to rebuild it but other than that I think it's fine. Is there any way I can double check everything? I'm really paranoid about my MacBook. It's my baby and I want to make sure there isn't something out of order that could be gimping the system.
Also, unrelated issue: Parallels had originally placed a "Windows Applications" folder in the dock. It was nice because I could see everything I had and when I clicked on one it would launch parallels automatically and launch that program. That folder is gone. Anyway I can get it back?

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