I havent had windows mess up on me from changing harddrives over from different computers since the days of win98 and early xp.
You should be able to change your motherboard, and it still boot up how it did before. You will just have to uninstall all drivers from the previus MB, its a good idea to do this before swapping them over. Then just use CCcleaner. You think Tom reinstalls windows and software everytime he does a different MB review
even if the HDD's are raided togeather as long the MB has the same Raid controller type. It will also work just turn the HDD's to raid mode in the bios and it will sort itself out.