I see what you're doing there and it's a very creative solution to the Vader misdirection problem. Maybe you just need to explain it better since you said you have other puzzle pieces you haven't laid out yet... but here's my read so far:
Cloning has to be reeled in somehow in the NPT. Cloning seems to be such a powerful technology that any fictional universe which contains the possibility of cloning would need to be almost exclusively about cloning.
Maybe let me phrase this as a question: Why don't we see any clones around the time of the OT? Maybe some of the Stormtrooper force is still made up of clones... and we're told that Boba Fett is actually a clone (whatevs!) but no one is talking about cloning Mon Mothma and replacing the head of the Alliance with an ersatz clone. When they capture Leia and torture her on the DS, why don't they just clone her and send the clone back to Alderaan or let Luke and Han rescue the clone. (Or didn't they? Hmm...) What the heck is Vader doing in his damaged, scarred, robot body if he could just order a new perfect one up from room service? Just like the early EU had something of a Superweapon problem, introducing cloning into Star Wars, unless it was somehow specifically restrained, would just overtake every Star Wars story. Think of world history since the US dropped the bombs in Japan- a large amount of it has been about keeping secret, reverse engineering, stockpiling, limiting production, etc. of atomic weapons.
Yet cloning, though unexplored, has been a part of the Star Wars fiction ever since Luke and Ben talked about the Clone Wars in A New Hope.
Conclusion: The prequels had to have cloning in them. The NPT has to have cloning in it. BUT, cloning should be restricted in some way as to explain why it's not any more widespread than it is. And then, the door on that technology must be more or less closed so that it is relatively a non-factor by the time the OT rolls around. I don't know how to introduce that door so that it can be closed in a series of movies made 30 years ago. But if you can figure that out, I think you'd be on your way to having a decent foundation upon which you can build your Clone Wars backdrop for a New Prequel Trilogy.