2 tips
when doing a checkdisk do it also checking for bad sector (I think) anyhow, that will give you 5 stages, and it will take up to twice the time, but it will find errors.
Also, copying your system 32 probably was more damaging, not to mention that the files won't match up with the ones that file protection has.
The other tip is that when a system doesn't boot I do this:
put the hard drive in another pc with antivirus and protection up to date, backup important data, run checkdisk in deep, run antivirus. If after that it still doesn't boot, just used the same installation disk that has been used for the OS installed, and do follow the instalation procedures until it asks to repair instalation (not the repair console). It will come after it does the detection of the OS. You will have to install all updates again, but it is better than not having the system running