Background
I'm doing system recovery on an old WinXP SP1 system brought to me on suspicion of virus infection. After taking preliminary backups, I used MalwareBytes to detect and clean the infection. I might've even gotten it all.

In the process, I've discovered (a) the system drive is showing signs of impending failure, and (b) the owner has been using the system's old crusty IE-6 instead of the up-to-date Firefox I've provided for him. So naturally, thinking I had a relatively stable system, I tried to hit the Windows Update site to install IE-8, in case further training doesn't stick.

The update site told me it needed to update the installer, and I started that process. Soon after, wuauclt.exe started crashing, reporting addresses in module esent.dll. There's a Microsoft KB (910437) on a problem with that DLL, so I downloaded the hotfix and installed. The crashing did not stop.

I attempted to install SP3 from the offline installer, but that didn't fix the issue either. The system is reporting a few hard drive / IDE controller errors, but they don't correlate to the crashes, so they aren't the direct cause. I've also attempted to rollback to the time between the infection removal and the first crashes, but that doesn't help.

Question
The hotfix I tried to install dealt with problem in transaction logs of the Extensible Storage Engine (ESE) database. I suspect this issue is similar, but that the database itself (whatever the ESE database is) is corrupted.

Is there a way to clean or clear this database so that system operation returns to normal? Can someone enlighten me as to what the ESE database actually is, and where it resides? Can I just locate some files and delete them to bring this under control?