Yes you're right on the script part.

Like I said I NEVER leave the keys out of the dev phase.

And then I'm good enough at tuning that I don't need to take 'em. So I'd start there.

One more thing to consider is that those FKS are self documenting the DB for you. It's much easier to hire a new guy and let him play with the db rather than explaining all the littles joins one at a time.