Wow, I don't think anybody saw this one coming.
My SIIG PCI USB host card seems to be the culprit!
POST never saw an issue but Windows 9x continued to randomly crash for no apparent reason and during boot at various points with no obvious cause.
However, I noticed that Windows 2000 would only freeze during file transfers, disk to disk or USB to disk. Initially this pointed to the mechanical hard disk being a problem, I always copy to the primary drive since it is larger. Replaced the Seagate 6GB drive with a WD Caviar and the problem persisted even after a reinstall.
Removing the old USB card seems to have fixed the problem and it boots and stays running reliably for now. Nothing is obviously wrong with the card and it appears to work fine in other machines but it will not be going back into the Vectra. I'll just have to find another USB adapter and in the meantime I will stick to diskettes and network transfers via Windows 2000.
Thanks everybody for the help and if anybody knows a reason why this card (SIIG JU-P20011) might have failed or would have caused this problem, I would be interested to hear about it.
RIP SIIG 2 port PCI host, 07/01 - 07/21.