My preference is for a clean install - these *usually* go smoothly with modern peripherals.
Upgrades can be unpredictable - particularly from one Microsoft operating system to another (!), although I found 98 to ME the smoothest upgrade I've ever done.
If you're doing a completely clean re-install, try adding each device one at a time, and only use the manufacturer's software once each device is installed and working, or if the device won't function without the manufacturer's driver (fairly rare).
If you need a manufacturer's driver at an early stage, don't run the setup utility on the CD-ROM, instead, search for the oemsetup.inf file on the CD, right click it and install it that way. Doing this ensures you get only the driver, not the full suite of software that can cause problems - especially under Windows 2000.
Upgrade the software components to manufaturer's one at a time, once you've got the system running stable. It's better to catch problems at the lowest possible level rather than install everything and not know where to start looking!
My preferred method is to go to the manufacturer's internet site, and download the most up-to-date driver for each component, rather than use the CDs that ship with the component.
I like to work from the ground up - ie, Motherboard/PCI bridge/USB root, etc, then disk subsystem (if any), communications (modem, printer), graphics, multimedia.
A PC's software make-up is like a house of cards - you balance one thing on top of another, until the whole thing collapses.
Therefore make sure the base is stable before piling stuff on top of it.
As an extra precaution, once the base system is stable, make a backup (or better still, a ghost image) and burn it to CD-R. That way you won't have to start from scratch the next time.
As I said earlier, VIA's can be *interesting* with W2k. At what point did W2k refuse to install? Any error messages?
Hope this helps - Good Luck!