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You should definitely adjust the intonation on the guitar saddles. The way to do this is to get a Strobe tuner, like a Peterson, and then play the 12th fret note, and then the 12th fret harmonic. They should be the exact same pitch. When you change the tension, gauge, or action of the strings, you should re-intonate, just to make sure you're in tune as much as possible.
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