Your best chance at solving this mystery is to focus on your hacked machine, how it was accessed, any malware that is on it. Mostly it sounds like you didn't secure your machine properly, in which case your chance of fixing this disaster will sadly be very small.
I believe it must have been a virus of some sorts. Yes you are right. I don't think I can do anything at this point. Format and reinstall windows is the best I can do, and from there on not ever use windows for any security sensitive sites/systems.
Just out of curiosity, I got a couple questions:
1) Do you have friends in real life who knew about your BTC activities and hoard of coins?
2) Did you ever let anyone touch or use your computer since you started involvement in BTC?
It could have very well been a virus and your BTC got stolen by some random pimply faced 13 y/o hacker in Russia or something, but often times thefts like this are perpetrated by people close to the victim, who had priveleged information and trust of the victim (kind of like an inside job).
Some people do know about my btc activities, but none of them have physicall access to my computer or otherwise. This happened right when I was sleeping with the doors locked. There is no way someone physically stole them. I am almost 100% sure this was done via some security hole in windows, trojan, or something like that. So yeah most likely some pimply faced teenage hacker now has them.
Ain't it wonderful? Free money for doing nothing. Who says crime doesn't pay.