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If the IDE controller is different, it will flip out and give you INACCESSIBLE_BOOT_DEVICE stop screen. (Hope I spelled that right haha) You'll see this in most situations when the chipset of the motherboard has changed. Easy way to get around it is to change your IDE drivers to the Standard IDE Controller drivers (granted this will make your system run slower since it won't be tweaked for the best IDE performance) but you should be able to boot into Windows after the motherboard switch then spend half the day updating drivers and rebooting.
The repair installation will basically run Windows setup without destroying anything. Boot to the CD, hit ENTER to say you want to install Windows. The next prompt will give you a chance to repair it. That's when you want to choose repair. I'd prefer this method over the above method since Windows will redetect all hardware and you won't have any "ghost" devices laying around causing potential problems in the future.
Good luck!
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