Touching the saddle is the last thing you'd do in a sequence of events to set up that guitar.
Flatten out the relief with the truss rod adjustment.
Get the nut slots cut to the proper depth (see Nut Action at Frets.com!).
Then & only then, take meat off the bottom of the saddle.
And before you do any of this, find out if the neck needs resetting, because if it does, you'll never get things right without doing that.
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