1. Turn off your computer
2. Open up the case, unplug the 1TB HDD. You can leave it seated in the case, just unplug it.
3. Plug in your clean SSD
4. Boot from Windows installation DVD or USB, install Windows cleanly onto your SSD.
5. Turn off your computer, plug in your 1TB HDD as well.
You will not lose any files in this way, and simply set your boot drive as your SSD rather than your HDD.