System process at 99% CPU

I built my current computer originally in late 1999 and early 2000. This computer was built part by part, with care taken in choosing each part. After a few months of instabilities due to the usual hardware incompatibilities and flakiness, I had a stable system. This system, for the most part, ran quite fine up to about October 19, 2002. At this point in time I was running Windows 2000, with service pack 2, exclusively.

The problem was that after leaving the computer on for anywhere between five and thirty hours, the computer would become very slow. The obvious reason for this was shown to me by the Windows Task Manager: the System process, which is always PID 8 on my computer, was using 99 percent of the CPU, and had been for many hours. And no, I am not referring to PID 0, the "System Idle Process", as many people on USENET have implied to others having this problem.

Below is the list of things I tried to fix this problem, and their results.
Action
 Result and observations
Attempt to kill the System process
 Windows refused to do this.
Close or kill all other processes
 After much delay, all processes were closed. However, the System process was still using 99% CPU.
Shut down the computer from the 'Start' menu
 After waiting for an hour, the computer still had not shut down.
Power down the computer by pressing the power switch for about a quarter second
 No effect.
Power down the computer by pressing the power switch down for four seconds
 Computer powers off. But the problem reappears anywhere from five to thirty hours later.
Run a virus scan
 No effect.
Replace the two to three year old 230W power supply with another two to three year old 235W power supply
 No effect.
Disable advanced power management in Windows control panel
 No effect.
Remove case lid to cool system better
 No effect.
Disable video acceleration in Windows
 No effect.
Disconnect computer from ethernet connection
 No effect.
Install proper monitor.inf file for my monitor, rather than using the default monitor driver
 No effect.
Disable APM (advanced power management) in the BIOS
 No effect.
Change 'system performance' setting in BIOS from 'optimal' to 'normal'
 No effect.
Disable CPU throttling in BIOS
 No effect.
Install Windows 2000 service pack 3
 No effect.
Try running the computer with many processes, including some CPU-intensive processes and leaving it Still crashes after the usual time period.
Try cold-booting the computer, then running it without even logging in.
 Still crashes after the usual time period. (November 2, 2002)
Back up all data, format all hard drives, reinstall Windows 2000 with service pack 3
 Still crashes after the usual time period. (November 11, 2002)
Replace power supply with a new 350W power supply with two fans (Nov.13)
 Still crashing, but takes perhaps twice as long to do so. Perhaps related to the fact that the second power supply fan points at the CPU
Replace CPU heat sink and fan with new heat sink and fan (Nov.19)
 No crash after 50 hours. Reboot to complete some software installs, no crash after another 182+ hours. System fixed.

My computer system specifications are (from memory):
HomeHome First written on Saturday, November 30, 2002.