As it's an old computer I would have started with a chkdsk /r to check the status of the HDD and then performed a sfc /scannow to check the file system if the chkdsk /r didn't report any KBs in bad sectors - have you done these pre-steps.
However, I'm not sure where you got the report that 10,000/400,000 items are messed up.
If they relate to the Package/Cat and Mum files then perhaps you would be better off factory resetting it so you're starting from scratch.
This will take it back to out of the box and then you will need to uninstall any bloatware that came preinstalled, including the trial version of whichever antivirus program was installed, using its uninstaller before you can install your own preference.
As the Package files relate to updates, then with an out of the box machine you would be installing all of the updates from scratch and that should resolve any Package file problems.