If I understand this correctly you're trying to swap a motherboard without reinstalling the OS entirely?

Hmm. To be honest, that's not very advisable with Win2k/XP. It's a lot like trying to replace the foundation of a house while leaving the rest of it in place. It can be done, but it's ugly. All of the devices on your system tend to be dependant on bus drivers and the PnP model that tend to be specific to the chipset your motherboard uses. So when you swap it out, Bad Things happen. You could get away with it in 95 and 98 because device access is more primitive - there wasn't any kind of hardware abstraction layer, for one.

Usually the problem boils down to two things: the HAL and your mass storage device. Swapping motherboards will usually work OK *if* those two things match between the boards. But that's rarely the case. I've learned from doing the unspeakable with sysprep, that you can often work around these problems, but it's not pretty. Basically you need to find out which HAL dll your new motherboard needs. Then take your hard drive and get it on another Win2k/XP machine (or a linux box that can read NTFS) and find the appropriate HAL file in %systemroot%\servicepackfiles\i386. Copy the right one into %systemroot%\system32 and rename it hal.dll. Unless you're going from a really old pre-ACPI system to an ACPI system, you should be OK. Otherwise the entire hardware enumeration in the system registry hive will be fubared and there's really anything you can do about it.

As far as the mass storage controller goes, you might get lucky. If both controllers are of a similar type, you might be able to boot succesfully and then change out the driver in a proper fashion. But if it can't find the boot device, you might try copying the correct device driver (ex. viaide.sys) to the name of your original mass storage driver and hope for the best. That's a really kludgy way of doing it, but if it gets your system to boot, you can then install the driver correctly.

For future reference, the best way to replace a motherboard on a Win2k/XP machine is to use the sysprep tool. It's supposed to be for cloning a computer to another more or less identical machine, but you can use it to transplant an existing installation of Windows to a totally dissimilar machine despite what MS says. The latest versions for XP and 2000 allow you to include a collection of mass storage drivers, which lets the OS cleanly load a correct driver after it emerges from sysprep. Then all you have to deal with is the hal.dll problem, which is pretty easy to fix.

Basically, before you replace the board, run sysprep on your computer and include the hard disk controller driver for the new board. It's a little complicated for Windows 2000, but there's a manual for it somewhere on Microsoft's site. When sysprep shuts down your computer, replace the motherboard. Then boot it back up and go through the mini-setup wizard that will do a complete redetection of your hardware. As far as I know, that's the cleanest way to transplant a Win2k/XP installation to a new body.