Re: Thoughts on Tonepros bridge and graphite nut
Is it acoustically dark as well? If not, I'd say change the pickup. I've found the Custom to be dark in some guitars, but very nice in others where other pickups were too bright.
If it's acoustically dark, then the bridge will affect the tone more than the nut, unless it's only dark on open strings.
If it's a bolt-on, you may also look at the pocket to ensure it's smooth and making good contact with the heel (bottom and end).
Unless the Tonepros bridge is made of steel, those locking studs aren't going to brighten it up. They'll just keep the bridge from falling off when you take off the strings and turn it upside down.
You may also want to see how much wobble the bridge studs have in their inserts. Too much means poor thread correlation, and thus poor contact, resulting in reduced highs.