While there is no cure to determine in all cases how a computer was damaged by a possible infection, there is a prevention mechanism. It is antivirus software. For whatever reasons, if you choose not to use one, you lend yourself to this type of situation. It's obviously very frustrating, so hopefully you can learn from that and implement some proper antivirus software that can help prevent you from getting back into another one of these situations.
Lots of people put lots of extra software on their machines and have no problems. These people are the ones that understand, respect, and implement the security measures necessary to keep their machines healthy. It doesn't take an illegal action on your computer to contract something that will degrade the OS. Sometimes all it takes is being on the wrong site at the wrong time or opening the wrong email. For these situations, antivirus helps prevent the headache that would have ensued once infected, as we've experienced here.