Hello ughi,
I can sympathise with you on this one, I've been in the same position and it's just maddening.
If you're getting error messages about the serial number it might be a corrupted registry entry, as can happen.
The more serious thing though is that checkdisk is running for several hours and not getting too far.
The first thing I have to ask you is:
Is there anything on the system you can't replace?
I have to ask that because if you do, then I'd let the repair run as long as it wants, then try booting it up and running SFC/SCANNOW. This will ask for your install CD and check that the critical system files are not damaged.
Myself I'd write it off as a bad job and reinstall windows, taking select format file system and not the quick version either.
Let it completely wipe what's there off and install a full fresh copy over the top. That is however because I generally don't keep material on my machine I can't replace so losing very little data in wiping the system.
As or the license key, you can either get one of the trial license keys off the web to get rid of it complaining about the key, and then use your official key again to get rid of the trial.