Ahem, i am not sure but based on the experiments that I did on Registry back then, the system file hold the information available in the "HKEY_LOCAL_MACHINE". It also contains a lot about the system configuration information which is synchronus in nature to many other registry entries. So it is really so very tough to make the system work the way it did before.

For example, just go to HKEY_LOCAL_MACHINE\Security hive, make the changes to the permission and restart the regedit program and see the changes. There are many many more thins and places in this hive which are not visible to us.

I think nihil is right. Better make the new installation the primary one. It is really very tough (if not impossible) to get the same behavior from the system as before corruption.