Take it from me, what you're planning is extremely problematic. There's no guarantee it'll work. Sometimes the smallest change in core hardware (chipset, IDE controller, etc.) and Windows will go nuts.
Only do it as a last resort. Formatting and installing fresh is the way to go. You'll have a nice, clean, virgin Windows registry with no legacy crap from your old machine (orphaned programs, missing files, etc.) Some people complain that they loose all those little tweaks they've made, but this just motivates them to make less tweaks, install less programs, do less customization -- in other words, be a minimalist. And really, there are no easy tweaks left that will significantly improve the performance of MS operating systems.
If you are forced into a situation where you don't have time for a fresh install, this procedure might help you:
1) Boot into Safe Mode.
2) Delete the WINDOWS/INF/OTHER folder.
3) Go to Control Panel > Add/Remove Programs and remove anything to do with the hardware in the current system -- video drivers, modem drivers, digital camera stuff, scanner TWAIN stuff, etc.
4) Run REGEDIT.
5) Delete the entire Enum branch of HKEY_LOCAL_MACHINE.
6) Under HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run and RunServices, look for anything hardware-related and remove it.
7) Shut down and install the new motherboard.
That's my procedure when I've had to do it in the past, but the success rate is still not terrific
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