After I rid a computer of a virus I take it offline,run scans from adaware,spybot,hijackthis.Then I run a duplicate and empty file searcher and clean that up manually.Then I run a registery cleaner then defrag the hard drive.Scan the boot sector and total machine again.Then and only then am I still 'unsure'if a virus is gone.
I'm being serious.One never knows if a cpu is clean.As far as I am concerned ,and in my opinion ,if you can get a virus then you may still have one unfound ,or a trojan waiting for a phone home command or a worm waiting for a set date etc...
Backup your data , cross your fingers and remember that it is just a machine with parts that you maintain.It will perform better with more maintanance and preventitive maintanance but no one online is ever truly safe from the junk thats out there.
Good luck and keep your chin up because if it can happen to you it can happen to us all.