Why do you want windows 2000? It's unsupported so you may well end up with stuff not running on it and being a pain for drivers etc, though a lot of XP drivers work on 2k. I can only find XP and Vista to buy
As for the second HDD idea it will work fine. I always have multiple partitions for my PCs, the C:\ partition only ever has the OS on it, all my games, downloads and other apps are in seperate partitions so when I do re-install windows all I lose is the OS and my links, sometimes I have to re-install the occassional app but a lot of the time they still work so all I do is create a new shortcut.
Never had the WGA issue myself but maybe they changed something since my last XP install as I swiped a legit serial from somewhere