Easiest thing to do would be to format the hard drive
Actually, it would be easier to do a "repair" installation of Windows XP.
Just boot straight to the WinXP CD, as if you are going to reinstall Windows. After the CD boots, you will be asked if you want to repair using the Recovery Console. This is *not* what you want, so proceed as if you are going to reinstall. You will then be given the option to "repair" Windows again, only this time, you are basically reinstalling Windows on top of itself. Hit "R" for repair, and the setup program will delete all your Windows system files and replace them with what is on the CD.
In my opinion, this is easier because it will leave the vast majority of your programs and data intact. You will still have to go back and install certain drivers, patches, Windows Update, etc., however.
By the way, something else I should ask is how similar or different the two motherboards are. If they use the same chipset, for example, then the problem is more likely to be the motherboard itself, or possibly some BIOS settings. It they are vastly different, though (like replacing a VIA chipset with NForce), then the problems are more likely to be software/driver related.