Reset or restore Windows Vista folder settings to default

Reset or restore Windows Vista folder settings to default

I had failing hard drive and managed to extract the data from it using
Linux. I have tried Macrium Reflect which wasn't successful, as the clone
failed. So, in Linux I finally managed to get the contents from the old
drive on the new one. The system boots fine with the new drive. However,
the permissions on the folders are different than before.
How I can reset them?
P.S. the old failing drive is still somewhat operational, I can get data
from it as external drive but can't boot from it (the machine loops on
POST, drive clicks, won't load at all). I managed to get image of it as
is, and can access its System Restore points. Unfortunately, it seems that
System Restore works per drive.
Thank you!