I think that you all are doing too much. The key point, although counterintuitive, is to pre-install all the NEW motherboard's drivers while running the OLD motherboard for the last time. Windows will ignore the new stuff because it then doesn't see any corresponding hardware. After you swap the motherboard and reboot, the Windows should ignore the old stuff and use the new. And if it doesn't, you can always boot the new system into safe mode and configure the drivers there.
I've done this 4 times without problems. In fact, I have one system whose hard disk has the leftovers from DOS 6 with DESQview(!)/Win 3.11/Win 95/Win 98/Win 98SE - each time I've upgraded the disk I started with a full disk-to-disk copy to keep the old system.
In other points, (1) make sure the old system is stable before you upgrade (Norton WinDoctor, registry checked, scan disked, etc.); (2) to keep your life simple, don't upgrade any unnecessary cards (graphics, modem, NIC, etc.) or devices (CD-ROM, DVD, ZipDisk, etc.) at the same time you change the motherboard. If (when) something goes wrong, you'll have minimized the range of possible causes.