One of the key factors that make our solid top guitars sound so good is the bone nut and saddle.A bone nut needs a little period of time to settle in. It also really benefits from having a simple graphite pencil rubbed in the slot. The graphite will lubricate the string and stop it from gripping as you tune it (ever hear your strings creak, creak, creak as you tune them?)
If you want to get your action height to the absolute lowest you should also get a trained Luthier to re-cut your nut slots. This will bring your action height down a little bit further than what can be achieved with reducing the height of the saddle.