Bob W.,
Naturally, there are all kinds of exhaustive tests you can run, but I see you eventually gave up and resorted to re-installing your operating system (OS); many others would have done the same. After all the other remedies you had tried, I would have also been really surprised to see the system still running so slowly. However, a few other possibilities come to mind:
(1) A boot sector virus or rootkit -- Based on my limited understanding of how boot sector malware sustains itself, I'm led to believe such infections can hide and survive efforts to eradicate the problem even if the hard drive is formatted and the OS is re-installed. If this is the case, consider using a utility that specifically targets rootkits. Alternatively, if you have a spare hard drive, consider re-doing the system installation using a different hard drive. Similarly, BIOS rootkits -- meaning malware hiding on your system's CMOS chip -- will linger even if you replace the hard drive, of course. If your CMOS is where the culprit resides, I'm not sure whether re-flashing the chip will necessarily fix the problem. If a CMOS infection is your problem, this may require further research.
(2) Re-infection -- Hopefully you're not transporting hardware drivers or data using infected media. If you're using a thumb drive, external drive, or even a CD/DVD that was already infected with hidden malware, then using these infected media during your system re-installation could also be the source of your problem.
(3) Hard disk controller drivers -- Check for updates to your hardware drivers, PARTICULARLY for your BIOS and hard disk controllers. I would NOT depend on the driver check available through the Windows device Properties / Drivers tab; many times I've found that check to be inadequate. Instead, I'd visit the Web site for the manufacturer of the device driver you're checking. It will take longer, but you'll almost certainly get better results. I have first hand experience in a case where adding a new hard drive to my computer severely bogged down my entire system all because the hard disk controllers needed a firmware update. I'd like to elaborate on this point a bit.
My computer had two physical disk drives; one had the OS and all my installed software, and I used the second drive for all my data. I also backed up my first hard drive to my second hard drive. Eventually, I replaced my second drive with a larger one. Everything seemed fine until I tried to back up my first drive to the new second hard drive for the first time. I couldn't believe it ... The backup that previously required just 25 minutes to complete now took more than three hours!?!? Fortunately, a little searching through the manufacturer's knowledge base uncovered obscure mention of this extreme performance problem. The recommended fix: check and update the firmware for the hard disk controller. It was a little tricky ... I had never done a BIOS or firmware update before, but the firmware update did the trick.
Oh, one more thing ... The problem I described where the firmware for the disk controller needed updating was also an XP system. There could be other causes for your problem, but based on my experiences, these that I've described would be my best guesses. Good luck and I hope you'll tell us what eventually fixes your system.
Tony M.