If your copy of windows is OEM it's tied to the original motherboard and will fail validation when moved to a new one. You can phone Microsoft to see if they'll let you do it, but I think they have tightened up on this.
If it's a retail copy of Windows you'll be fine.
I am not sure if simply cloning your HDD will work since you're swapping the mobo at the same time.
You could get new SATA optical drives instead and attach your current HDD's to the IDE socket (cheaper but slower option)