I'm an independant software developer--- I can't say that there aren't any disc based solutions to what you are trying to do--- in fact I know, (such as Starforce), but these methods are usually employed by the big name game developers to protect their products (Civ 4, Splinter Cell--- etc)--- I've never seen anyone at the utility level protect their software in such a way.
No matter what you do it seems like you are going a little over the top to protect your work--- I understand the desire to do this, but at the basic level, even clone disc will copy a protected cd, warts and all----
You'd be better off spending that time improving the product than trying to prevent people from copying it--- not to mention the fact software such as this is freely available on the internet.
Good luck.