Before you go down the path of reinstalling Windows you could try running something like CCleaner (from here:
http://www.piriform.com/CCLEANER ) and running a registry scan and fix to see if that helps.
If you are going to reinstall Windows then I would suggest disconnecting all but the Primary HDD (the one you want to install onto) and your DVD/CD drive.
I'm not sure what you are referring to when you talk about registering Windows but if you mean Activation then you shouldn't have a problem and you can mark the box to Automatically Activate when Windows is on-line during the install process. Once you have installed windows you can reconnect your other HDD's and they should be automatically detected when you start-up. You will probably have to restart the PC once windows has installed their drivers.
You will then need to install the Motherboard drivers and the drivers for any other hardware that you have installed and then comes then fun of downloading ALL of the Windows updates (oh joy!)
If you have installed any programmes/software these will need to be reinstalled and possibly updated, once you have Windows up and running again.