I think I can answer one question. The 60GB won't boot without the 1TB because of the 100MB partition on disk3. Windows uses a small system partition that you can put wherever you want and iBuyPower must have kept that partition off the SSD to save space. Also, if I had to guess, the FOR WINDOWS 2 partition on disk3 could be where they put the page file.
I would imagine there's ways of cleaning it all up so that everything works the way you want, but the only headache-free way is going to be with a fresh install. I know that can be scary, but backing up your data and putting a new installation on the 120GB drive is the most reliable way. If you do that, I suggest unplugging your 1TB drives before hand because the windows installer might see that there is a 100MB system partition on the 1TB drive and try to automatically put the next one there.