Check the intonation as follows: tune the guitar to normal pitch. Checking the open string and the 12th fret harmonic is NOT the correct way to check/set intonation. You must compare the 12th fret harmonic with the FRETTED note at the 12th fret, not with the open string. When all six strings agree with each other in this measurement, THEN your intonation will be close to "perfect".
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Put the stop bar back in place, make sure you put the bridge on correctly (check the saddles, they should be further away from the pickups on the bass side, closer on the treble side).
Check the intonation as follows: tune the guitar to normal pitch. Checking the open string and the 12th fret harmonic is NOT the correct way to check/set intonation. You must compare the 12th fret harmonic with the FRETTED note at the 12th fret, not with the open string. When all six strings agree with each other in this measurement, THEN your intonation will be close to "perfect".
Check the intonation as follows: tune the guitar to normal pitch. Checking the open string and the 12th fret harmonic is NOT the correct way to check/set intonation. You must compare the 12th fret harmonic with the FRETTED note at the 12th fret, not with the open string. When all six strings agree with each other in this measurement, THEN your intonation will be close to "perfect".