Right, I think I'm a bit lost myself.
You're going to give copies of your website to a thousand people, each one hosted on its own domain?
So what do your affiliates do? Will they be allowed to distinguish the sites that you've given them from each other?
As I say, it's almost certain that unless the sites are substantially different, Google will see them as duplicated content.
Well, alright, not substantially different, but at least not identical.